diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 01bd13a9e9..8521c44100 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: v0.4.5
+    rev: v0.4.6
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ae43fd4e7b..63bef50b84 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@
 - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))
 - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
 - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]