diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000000..1c28f0b3d7
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,25 @@
+name: Lint
+
+on:
+  push:
+    branches: [main, 3.1.x]
+  pull_request:
+    branches: [main, 3.1.x]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Install prek
+        run: uv tool install prek
+      - name: Run prek
+        run: prek run --all-files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c4132530af..f85b500784 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,8 +1,9 @@
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autoupdate_schedule: "monthly"
-  autofix_commit_msg: "style: pre-commit fixes"
   autofix_prs: false
+  skip: []  # pre-commit.ci only checks for updates, prek runs hooks locally
+
 default_stages: [pre-commit, pre-push]
 
 default_language_version:
diff --git a/changes/3658.misc.md b/changes/3658.misc.md
new file mode 100644
index 0000000000..f400d97473
--- /dev/null
+++ b/changes/3658.misc.md
@@ -0,0 +1 @@
+Switch from `pre-commit` to [`prek`](https://github.com/j178/prek) for pre-commit checks.
\ No newline at end of file
diff --git a/docs/contributing.md b/docs/contributing.md
index e42ba0edf1..c330504536 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -109,26 +109,50 @@ All tests are automatically run via GitHub Actions for every pull request and mu
 
 > **Note:** Previous versions of Zarr-Python made extensive use of doctests. These tests were not maintained during the 3.0 refactor but may be brought back in the future. See issue #2614 for more details.
 
-### Code standards - using pre-commit
+### Code standards - using prek
 
 All code must conform to the PEP8 standard. Regarding line length, lines up to 100 characters are allowed, although please try to keep under 90 wherever possible.
 
-`Zarr` uses a set of `pre-commit` hooks and the `pre-commit` bot to format, type-check, and prettify the codebase. `pre-commit` can be installed locally by running:
+`Zarr` uses a set of git hooks managed by [`prek`](https://github.com/j178/prek), a fast, Rust-based pre-commit hook manager that is fully compatible with `.pre-commit-config.yaml` files. `prek` can be installed locally by running:
 
 ```bash
-python -m pip install pre-commit
+uv tool install prek
+```
+
+or:
+
+```bash
+pip install prek
 ```
 
 The hooks can be installed locally by running:
 
 ```bash
-pre-commit install
+prek install
+```
+
+This would run the checks every time a commit is created locally. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running:
+
+```bash
+prek run --all-files
+```
+
+You can also run hooks only for files in a specific directory:
+
+```bash
+prek run --directory src/zarr
+```
+
+Or run hooks for files changed in the last commit:
+
+```bash
+prek run --last-commit
 ```
 
-This would run the checks every time a commit is created locally. These checks will also run on every commit pushed to an open PR, resulting in some automatic styling fixes by the `pre-commit` bot. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running:
+To list all available hooks:
 
 ```bash
-pre-commit run --all-files
+prek list
 ```
 
 If you would like to skip the failing checks and push the code for further discussion, use the `--no-verify` option with `git commit`.
diff --git a/pyproject.toml b/pyproject.toml
index e09bab4cb9..068caa1f0d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,7 @@ maintainers = [
     { name = "Deepak Cherian" }
 ]
 requires-python = ">=3.11"
-# If you add a new dependency here, please also add it to .pre-commit-config.yml
+# If you add a new dependency here, please also add it to .pre-commit-config.yaml
 dependencies = [
     'packaging>=22.0',
     'numpy>=2.0',
@@ -428,6 +428,7 @@ markers = [
 ignore = [
 	"PC111",  # fix Python code in documentation - enable later
 	"PC180",  # for JavaScript - not interested
+	"PC902",  # pre-commit.ci custom autofix message - not using autofix
 ]
 
 [tool.numpydoc_validation]