diff --git a/README.md b/README.md
index 1a0f6b1c4..6da46c00e 100644
--- a/README.md
+++ b/README.md
@@ -751,6 +751,7 @@ The following sets of tools are available:
 
 - **assign_copilot_to_issue** - Assign Copilot to issue
   - **Required OAuth Scopes**: `repo`
+  - `base_ref`: Git reference (e.g., branch) that the agent will start its work from. If not specified, defaults to the repository's default branch (string, optional)
   - `issue_number`: Issue number (number, required)
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
diff --git a/internal/ghmcp/server.go b/internal/ghmcp/server.go
index 165886606..250f6b4cc 100644
--- a/internal/ghmcp/server.go
+++ b/internal/ghmcp/server.go
@@ -622,6 +622,12 @@ type bearerAuthTransport struct {
 func (t *bearerAuthTransport) RoundTrip(req *http.Request) (*http.Response, error) {
 	req = req.Clone(req.Context())
 	req.Header.Set("Authorization", "Bearer "+t.token)
+
+	// Check for GraphQL-Features in context and add header if present
+	if features := github.GetGraphQLFeatures(req.Context()); len(features) > 0 {
+		req.Header.Set("GraphQL-Features", strings.Join(features, ", "))
+	}
+
 	return t.transport.RoundTrip(req)
 }
 
diff --git a/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap b/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap
index 354600147..7ad1922a0 100644
--- a/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap
+++ b/pkg/github/__toolsnaps__/assign_copilot_to_issue.snap
@@ -7,6 +7,10 @@
   "inputSchema": {
     "type": "object",
     "properties": {
+      "base_ref": {
+        "type": "string",
+        "description": "Git reference (e.g., branch) that the agent will start its work from. If not specified, defaults to the repository's default branch"
+      },
       "issue_number": {
         "type": "number",
         "description": "Issue number"
diff --git a/pkg/github/issues.go b/pkg/github/issues.go
index 1e29a0eef..63174c9e9 100644
--- a/pkg/github/issues.go
+++ b/pkg/github/issues.go
@@ -1646,6 +1646,10 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 						Type:        "number",
 						Description: "Issue number",
 					},
+					"base_ref": {
+						Type:        "string",
+						Description: "Git reference (e.g., branch) that the agent will start its work from. If not specified, defaults to the repository's default branch",
+					},
 				},
 				Required: []string{"owner", "repo", "issue_number"},
 			},
@@ -1656,6 +1660,7 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 				Owner       string `mapstructure:"owner"`
 				Repo        string `mapstructure:"repo"`
 				IssueNumber int32  `mapstructure:"issue_number"`
+				BaseRef     string `mapstructure:"base_ref"`
 			}
 			if err := mapstructure.Decode(args, &params); err != nil {
 				return utils.NewToolResultError(err.Error()), nil, nil
@@ -1724,10 +1729,10 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 				return utils.NewToolResultError("copilot isn't available as an assignee for this issue. Please inform the user to visit https://docs.github.com/en/copilot/using-github-copilot/using-copilot-coding-agent-to-work-on-tasks/about-assigning-tasks-to-copilot for more information."), nil, nil
 			}
 
-			// Next let's get the GQL Node ID and current assignees for this issue because the only way to
-			// assign copilot is to use replaceActorsForAssignable which requires the full list.
+			// Next, get the issue ID and repository ID
 			var getIssueQuery struct {
 				Repository struct {
+					ID    githubv4.ID
 					Issue struct {
 						ID        githubv4.ID
 						Assignees struct {
@@ -1749,30 +1754,54 @@ func AssignCopilotToIssue(t translations.TranslationHelperFunc) inventory.Server
 				return ghErrors.NewGitHubGraphQLErrorResponse(ctx, "failed to get issue ID", err), nil, nil
 			}
 
-			// Finally, do the assignment. Just for reference, assigning copilot to an issue that it is already
-			// assigned to seems to have no impact (which is a good thing).
-			var assignCopilotMutation struct {
-				ReplaceActorsForAssignable struct {
-					Typename string `graphql:"__typename"` // Not required but we need a selector or GQL errors
-				} `graphql:"replaceActorsForAssignable(input: $input)"`
-			}
-
+			// Build the assignee IDs list including copilot
 			actorIDs := make([]githubv4.ID, len(getIssueQuery.Repository.Issue.Assignees.Nodes)+1)
 			for i, node := range getIssueQuery.Repository.Issue.Assignees.Nodes {
 				actorIDs[i] = node.ID
 			}
 			actorIDs[len(getIssueQuery.Repository.Issue.Assignees.Nodes)] = copilotAssignee.ID
 
+			// Prepare agent assignment input
+			emptyString := githubv4.String("")
+			agentAssignment := &AgentAssignmentInput{
+				CustomAgent:        &emptyString,
+				CustomInstructions: &emptyString,
+				TargetRepositoryID: getIssueQuery.Repository.ID,
+			}
+
+			// Add base ref if provided
+			if params.BaseRef != "" {
+				baseRef := githubv4.String(params.BaseRef)
+				agentAssignment.BaseRef = &baseRef
+			}
+
+			// Execute the updateIssue mutation with the GraphQL-Features header
+			// This header is required for the agent assignment API which is not GA yet
+			var updateIssueMutation struct {
+				UpdateIssue struct {
+					Issue struct {
+						ID     githubv4.ID
+						Number githubv4.Int
+						URL    githubv4.String
+					}
+				} `graphql:"updateIssue(input: $input)"`
+			}
+
+			// Add the GraphQL-Features header for the agent assignment API
+			// The header will be read by the HTTP transport if it's configured to do so
+			ctxWithFeatures := withGraphQLFeatures(ctx, "issues_copilot_assignment_api_support")
+
 			if err := client.Mutate(
-				ctx,
-				&assignCopilotMutation,
-				ReplaceActorsForAssignableInput{
-					AssignableID: getIssueQuery.Repository.Issue.ID,
-					ActorIDs:     actorIDs,
+				ctxWithFeatures,
+				&updateIssueMutation,
+				UpdateIssueInput{
+					ID:              getIssueQuery.Repository.Issue.ID,
+					AssigneeIDs:     actorIDs,
+					AgentAssignment: agentAssignment,
 				},
 				nil,
 			); err != nil {
-				return nil, nil, fmt.Errorf("failed to replace actors for assignable: %w", err)
+				return nil, nil, fmt.Errorf("failed to update issue with agent assignment: %w", err)
 			}
 
 			return utils.NewToolResultText("successfully assigned copilot to issue"), nil, nil
@@ -1784,6 +1813,21 @@ type ReplaceActorsForAssignableInput struct {
 	ActorIDs     []githubv4.ID `json:"actorIds"`
 }
 
+// AgentAssignmentInput represents the input for assigning an agent to an issue.
+type AgentAssignmentInput struct {
+	BaseRef            *githubv4.String `json:"baseRef,omitempty"`
+	CustomAgent        *githubv4.String `json:"customAgent,omitempty"`
+	CustomInstructions *githubv4.String `json:"customInstructions,omitempty"`
+	TargetRepositoryID githubv4.ID      `json:"targetRepositoryId"`
+}
+
+// UpdateIssueInput represents the input for updating an issue with agent assignment.
+type UpdateIssueInput struct {
+	ID              githubv4.ID           `json:"id"`
+	AssigneeIDs     []githubv4.ID         `json:"assigneeIds"`
+	AgentAssignment *AgentAssignmentInput `json:"agentAssignment,omitempty"`
+}
+
 // parseISOTimestamp parses an ISO 8601 timestamp string into a time.Time object.
 // Returns the parsed time or an error if parsing fails.
 // Example formats supported: "2023-01-15T14:30:00Z", "2023-01-15"
@@ -1869,3 +1913,19 @@ func AssignCodingAgentPrompt(t translations.TranslationHelperFunc) inventory.Ser
 		},
 	)
 }
+
+// graphQLFeaturesKey is a context key for GraphQL feature flags
+type graphQLFeaturesKey struct{}
+
+// withGraphQLFeatures adds GraphQL feature flags to the context
+func withGraphQLFeatures(ctx context.Context, features ...string) context.Context {
+	return context.WithValue(ctx, graphQLFeaturesKey{}, features)
+}
+
+// GetGraphQLFeatures retrieves GraphQL feature flags from the context
+func GetGraphQLFeatures(ctx context.Context) []string {
+	if features, ok := ctx.Value(graphQLFeaturesKey{}).([]string); ok {
+		return features
+	}
+	return nil
+}
diff --git a/pkg/github/issues_test.go b/pkg/github/issues_test.go
index 2ccd4918f..21e78874a 100644
--- a/pkg/github/issues_test.go
+++ b/pkg/github/issues_test.go
@@ -2085,8 +2085,15 @@ func TestAssignCopilotToIssue(t *testing.T) {
 	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "owner")
 	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "repo")
 	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "issue_number")
+	assert.Contains(t, tool.InputSchema.(*jsonschema.Schema).Properties, "base_ref")
 	assert.ElementsMatch(t, tool.InputSchema.(*jsonschema.Schema).Required, []string{"owner", "repo", "issue_number"})
 
+	// Helper function to create pointer to githubv4.String
+	ptrGitHubv4String := func(s string) *githubv4.String {
+		v := githubv4.String(s)
+		return &v
+	}
+
 	var pageOfFakeBots = func(n int) []struct{} {
 		// We don't _really_ need real bots here, just objects that count as entries for the page
 		bots := make([]struct{}, n)
@@ -2151,6 +2158,7 @@ func TestAssignCopilotToIssue(t *testing.T) {
 				githubv4mock.NewQueryMatcher(
 					struct {
 						Repository struct {
+							ID    githubv4.ID
 							Issue struct {
 								ID        githubv4.ID
 								Assignees struct {
@@ -2168,6 +2176,7 @@ func TestAssignCopilotToIssue(t *testing.T) {
 					},
 					githubv4mock.DataResponse(map[string]any{
 						"repository": map[string]any{
+							"id": githubv4.ID("test-repo-id"),
 							"issue": map[string]any{
 								"id": githubv4.ID("test-issue-id"),
 								"assignees": map[string]any{
@@ -2179,16 +2188,34 @@ func TestAssignCopilotToIssue(t *testing.T) {
 				),
 				githubv4mock.NewMutationMatcher(
 					struct {
-						ReplaceActorsForAssignable struct {
-							Typename string `graphql:"__typename"`
-						} `graphql:"replaceActorsForAssignable(input: $input)"`
+						UpdateIssue struct {
+							Issue struct {
+								ID     githubv4.ID
+								Number githubv4.Int
+								URL    githubv4.String
+							}
+						} `graphql:"updateIssue(input: $input)"`
 					}{},
-					ReplaceActorsForAssignableInput{
-						AssignableID: githubv4.ID("test-issue-id"),
-						ActorIDs:     []githubv4.ID{githubv4.ID("copilot-swe-agent-id")},
+					UpdateIssueInput{
+						ID:          githubv4.ID("test-issue-id"),
+						AssigneeIDs: []githubv4.ID{githubv4.ID("copilot-swe-agent-id")},
+						AgentAssignment: &AgentAssignmentInput{
+							BaseRef:            nil,
+							CustomAgent:        ptrGitHubv4String(""),
+							CustomInstructions: ptrGitHubv4String(""),
+							TargetRepositoryID: githubv4.ID("test-repo-id"),
+						},
 					},
 					nil,
-					githubv4mock.DataResponse(map[string]any{}),
+					githubv4mock.DataResponse(map[string]any{
+						"updateIssue": map[string]any{
+							"issue": map[string]any{
+								"id":     githubv4.ID("test-issue-id"),
+								"number": githubv4.Int(123),
+								"url":    githubv4.String("https://github.com/owner/repo/issues/123"),
+							},
+						},
+					}),
 				),
 			),
 		},
@@ -2240,6 +2267,7 @@ func TestAssignCopilotToIssue(t *testing.T) {
 				githubv4mock.NewQueryMatcher(
 					struct {
 						Repository struct {
+							ID    githubv4.ID
 							Issue struct {
 								ID        githubv4.ID
 								Assignees struct {
@@ -2257,6 +2285,7 @@ func TestAssignCopilotToIssue(t *testing.T) {
 					},
 					githubv4mock.DataResponse(map[string]any{
 						"repository": map[string]any{
+							"id": githubv4.ID("test-repo-id"),
 							"issue": map[string]any{
 								"id": githubv4.ID("test-issue-id"),
 								"assignees": map[string]any{
@@ -2275,20 +2304,38 @@ func TestAssignCopilotToIssue(t *testing.T) {
 				),
 				githubv4mock.NewMutationMatcher(
 					struct {
-						ReplaceActorsForAssignable struct {
-							Typename string `graphql:"__typename"`
-						} `graphql:"replaceActorsForAssignable(input: $input)"`
+						UpdateIssue struct {
+							Issue struct {
+								ID     githubv4.ID
+								Number githubv4.Int
+								URL    githubv4.String
+							}
+						} `graphql:"updateIssue(input: $input)"`
 					}{},
-					ReplaceActorsForAssignableInput{
-						AssignableID: githubv4.ID("test-issue-id"),
-						ActorIDs: []githubv4.ID{
+					UpdateIssueInput{
+						ID: githubv4.ID("test-issue-id"),
+						AssigneeIDs: []githubv4.ID{
 							githubv4.ID("existing-assignee-id"),
 							githubv4.ID("existing-assignee-id-2"),
 							githubv4.ID("copilot-swe-agent-id"),
 						},
+						AgentAssignment: &AgentAssignmentInput{
+							BaseRef:            nil,
+							CustomAgent:        ptrGitHubv4String(""),
+							CustomInstructions: ptrGitHubv4String(""),
+							TargetRepositoryID: githubv4.ID("test-repo-id"),
+						},
 					},
 					nil,
-					githubv4mock.DataResponse(map[string]any{}),
+					githubv4mock.DataResponse(map[string]any{
+						"updateIssue": map[string]any{
+							"issue": map[string]any{
+								"id":     githubv4.ID("test-issue-id"),
+								"number": githubv4.Int(123),
+								"url":    githubv4.String("https://github.com/owner/repo/issues/123"),
+							},
+						},
+					}),
 				),
 			),
 		},
@@ -2377,6 +2424,7 @@ func TestAssignCopilotToIssue(t *testing.T) {
 				githubv4mock.NewQueryMatcher(
 					struct {
 						Repository struct {
+							ID    githubv4.ID
 							Issue struct {
 								ID        githubv4.ID
 								Assignees struct {
@@ -2394,6 +2442,7 @@ func TestAssignCopilotToIssue(t *testing.T) {
 					},
 					githubv4mock.DataResponse(map[string]any{
 						"repository": map[string]any{
+							"id": githubv4.ID("test-repo-id"),
 							"issue": map[string]any{
 								"id": githubv4.ID("test-issue-id"),
 								"assignees": map[string]any{
@@ -2405,16 +2454,34 @@ func TestAssignCopilotToIssue(t *testing.T) {
 				),
 				githubv4mock.NewMutationMatcher(
 					struct {
-						ReplaceActorsForAssignable struct {
-							Typename string `graphql:"__typename"`
-						} `graphql:"replaceActorsForAssignable(input: $input)"`
+						UpdateIssue struct {
+							Issue struct {
+								ID     githubv4.ID
+								Number githubv4.Int
+								URL    githubv4.String
+							}
+						} `graphql:"updateIssue(input: $input)"`
 					}{},
-					ReplaceActorsForAssignableInput{
-						AssignableID: githubv4.ID("test-issue-id"),
-						ActorIDs:     []githubv4.ID{githubv4.ID("copilot-swe-agent-id")},
+					UpdateIssueInput{
+						ID:          githubv4.ID("test-issue-id"),
+						AssigneeIDs: []githubv4.ID{githubv4.ID("copilot-swe-agent-id")},
+						AgentAssignment: &AgentAssignmentInput{
+							BaseRef:            nil,
+							CustomAgent:        ptrGitHubv4String(""),
+							CustomInstructions: ptrGitHubv4String(""),
+							TargetRepositoryID: githubv4.ID("test-repo-id"),
+						},
 					},
 					nil,
-					githubv4mock.DataResponse(map[string]any{}),
+					githubv4mock.DataResponse(map[string]any{
+						"updateIssue": map[string]any{
+							"issue": map[string]any{
+								"id":     githubv4.ID("test-issue-id"),
+								"number": githubv4.Int(123),
+								"url":    githubv4.String("https://github.com/owner/repo/issues/123"),
+							},
+						},
+					}),
 				),
 			),
 		},
@@ -2461,6 +2528,116 @@ func TestAssignCopilotToIssue(t *testing.T) {
 			expectToolError:    true,
 			expectedToolErrMsg: "copilot isn't available as an assignee for this issue. Please inform the user to visit https://docs.github.com/en/copilot/using-github-copilot/using-copilot-coding-agent-to-work-on-tasks/about-assigning-tasks-to-copilot for more information.",
 		},
+		{
+			name: "successful assignment with base_ref specified",
+			requestArgs: map[string]any{
+				"owner":        "owner",
+				"repo":         "repo",
+				"issue_number": float64(123),
+				"base_ref":     "feature-branch",
+			},
+			mockedClient: githubv4mock.NewMockedHTTPClient(
+				githubv4mock.NewQueryMatcher(
+					struct {
+						Repository struct {
+							SuggestedActors struct {
+								Nodes []struct {
+									Bot struct {
+										ID       githubv4.ID
+										Login    githubv4.String
+										TypeName string `graphql:"__typename"`
+									} `graphql:"... on Bot"`
+								}
+								PageInfo struct {
+									HasNextPage bool
+									EndCursor   string
+								}
+							} `graphql:"suggestedActors(first: 100, after: $endCursor, capabilities: CAN_BE_ASSIGNED)"`
+						} `graphql:"repository(owner: $owner, name: $name)"`
+					}{},
+					map[string]any{
+						"owner":     githubv4.String("owner"),
+						"name":      githubv4.String("repo"),
+						"endCursor": (*githubv4.String)(nil),
+					},
+					githubv4mock.DataResponse(map[string]any{
+						"repository": map[string]any{
+							"suggestedActors": map[string]any{
+								"nodes": []any{
+									map[string]any{
+										"id":         githubv4.ID("copilot-swe-agent-id"),
+										"login":      githubv4.String("copilot-swe-agent"),
+										"__typename": "Bot",
+									},
+								},
+							},
+						},
+					}),
+				),
+				githubv4mock.NewQueryMatcher(
+					struct {
+						Repository struct {
+							ID    githubv4.ID
+							Issue struct {
+								ID        githubv4.ID
+								Assignees struct {
+									Nodes []struct {
+										ID githubv4.ID
+									}
+								} `graphql:"assignees(first: 100)"`
+							} `graphql:"issue(number: $number)"`
+						} `graphql:"repository(owner: $owner, name: $name)"`
+					}{},
+					map[string]any{
+						"owner":  githubv4.String("owner"),
+						"name":   githubv4.String("repo"),
+						"number": githubv4.Int(123),
+					},
+					githubv4mock.DataResponse(map[string]any{
+						"repository": map[string]any{
+							"id": githubv4.ID("test-repo-id"),
+							"issue": map[string]any{
+								"id": githubv4.ID("test-issue-id"),
+								"assignees": map[string]any{
+									"nodes": []any{},
+								},
+							},
+						},
+					}),
+				),
+				githubv4mock.NewMutationMatcher(
+					struct {
+						UpdateIssue struct {
+							Issue struct {
+								ID     githubv4.ID
+								Number githubv4.Int
+								URL    githubv4.String
+							}
+						} `graphql:"updateIssue(input: $input)"`
+					}{},
+					UpdateIssueInput{
+						ID:          githubv4.ID("test-issue-id"),
+						AssigneeIDs: []githubv4.ID{githubv4.ID("copilot-swe-agent-id")},
+						AgentAssignment: &AgentAssignmentInput{
+							BaseRef:            ptrGitHubv4String("feature-branch"),
+							CustomAgent:        ptrGitHubv4String(""),
+							CustomInstructions: ptrGitHubv4String(""),
+							TargetRepositoryID: githubv4.ID("test-repo-id"),
+						},
+					},
+					nil,
+					githubv4mock.DataResponse(map[string]any{
+						"updateIssue": map[string]any{
+							"issue": map[string]any{
+								"id":     githubv4.ID("test-issue-id"),
+								"number": githubv4.Int(123),
+								"url":    githubv4.String("https://github.com/owner/repo/issues/123"),
+							},
+						},
+					}),
+				),
+			),
+		},
 	}
 
 	for _, tc := range tests {