diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e0c243c029..b9920b2701 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.0
+    rev: v0.12.1
     hooks:
       - id: ruff-check # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ffe58d76c2..34b1411da7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -39,6 +39,7 @@
 - Give unique button ids to help buttons in create app ([#3645](https://github.com/nf-core/tools/pull/3645))
 - Parallelize pytest runs and speed up coverage step ([#3635](https://github.com/nf-core/tools/pull/3635))
 - Update gitpod/workspace-base Docker digest to 77021d8 ([#3649](https://github.com/nf-core/tools/pull/3649))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.1 ([#3648](https://github.com/nf-core/tools/pull/3648))
 
 ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02]