diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7311b5a9a3f..926be8b5175 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -46,3 +46,4 @@ repos:
           - file
           - python
         exclude: vendored
+        args: [--config, python/setup.cfg]
diff --git a/dev/archery/archery/utils/lint.py b/dev/archery/archery/utils/lint.py
index d4879be79ad..ab9eb97754c 100644
--- a/dev/archery/archery/utils/lint.py
+++ b/dev/archery/archery/utils/lint.py
@@ -230,6 +230,7 @@ def python_linter(src, fix=False):
 
     yield LintResult.from_cmd(
         flake8("--extend-exclude=" + ','.join(flake8_exclude),
+               "--config=" + os.path.join(src.python, "setup.cfg"),
                setup_py, src.pyarrow, os.path.join(src.python, "examples"),
                src.dev, check=False))