diff --git a/python/codeql-extractor.yml b/python/codeql-extractor.yml
index 97a9e1f2cf2f..2bd1a9c0aa76 100644
--- a/python/codeql-extractor.yml
+++ b/python/codeql-extractor.yml
@@ -44,3 +44,10 @@ options:
       Use this setting with caution, the Python extractor requires Python 3 to run.
     type: string
     pattern: "^(py|python|python3)$"
+  skip_hidden_directories:
+    title: Controls whether hidden directories are skipped during extraction.
+    description: >
+      By default, CodeQL will extract all Python files, including ones located in hidden directories. By setting this option to true, these hidden directories will be skipped instead.
+      Accepted values are true and false.
+    type: string
+    pattern: "^(true|false)$"
diff --git a/python/extractor/cli-integration-test/hidden-files/query-default.expected b/python/extractor/cli-integration-test/hidden-files/query-default.expected
new file mode 100644
index 000000000000..cc92af624b37
--- /dev/null
+++ b/python/extractor/cli-integration-test/hidden-files/query-default.expected
@@ -0,0 +1,5 @@
+|             name              |
++-------------------------------+
+| .hidden_file.py               |
+| foo.py                        |
+| visible_file_in_hidden_dir.py |
diff --git a/python/extractor/cli-integration-test/hidden-files/query-skipped.expected b/python/extractor/cli-integration-test/hidden-files/query-skipped.expected
new file mode 100644
index 000000000000..688dbe00d570
--- /dev/null
+++ b/python/extractor/cli-integration-test/hidden-files/query-skipped.expected
@@ -0,0 +1,4 @@
+|      name       |
++-----------------+
+| .hidden_file.py |
+| foo.py          |
diff --git a/python/extractor/cli-integration-test/hidden-files/query.ql b/python/extractor/cli-integration-test/hidden-files/query.ql
new file mode 100644
index 000000000000..3b1b3c03849b
--- /dev/null
+++ b/python/extractor/cli-integration-test/hidden-files/query.ql
@@ -0,0 +1,3 @@
+import python
+
+select any(File f).getShortName() as name order by name
diff --git a/python/extractor/cli-integration-test/hidden-files/repo_dir/.hidden_dir/visible_file_in_hidden_dir.py b/python/extractor/cli-integration-test/hidden-files/repo_dir/.hidden_dir/visible_file_in_hidden_dir.py
new file mode 100644
index 000000000000..e69de29bb2d1
diff --git a/python/extractor/cli-integration-test/hidden-files/repo_dir/.hidden_file.py b/python/extractor/cli-integration-test/hidden-files/repo_dir/.hidden_file.py
new file mode 100644
index 000000000000..e69de29bb2d1
diff --git a/python/extractor/cli-integration-test/hidden-files/repo_dir/foo.py b/python/extractor/cli-integration-test/hidden-files/repo_dir/foo.py
new file mode 100644
index 000000000000..517b47df53c2
--- /dev/null
+++ b/python/extractor/cli-integration-test/hidden-files/repo_dir/foo.py
@@ -0,0 +1 @@
+print(42)
diff --git a/python/extractor/cli-integration-test/hidden-files/test.sh b/python/extractor/cli-integration-test/hidden-files/test.sh
new file mode 100755
index 000000000000..77cb12664af6
--- /dev/null
+++ b/python/extractor/cli-integration-test/hidden-files/test.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+set -Eeuo pipefail # see https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/
+
+set -x
+
+CODEQL=${CODEQL:-codeql}
+
+SCRIPTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+cd "$SCRIPTDIR"
+
+rm -rf db db-skipped
+
+# Test 1: Default behavior should be to extract files in hidden directories
+$CODEQL database create db --language python --source-root repo_dir/
+$CODEQL query run --database db query.ql > query-default.actual
+diff query-default.expected query-default.actual
+
+# Test 2: Setting the relevant extractor option to true skips files in hidden directories
+$CODEQL database create db-skipped --language python --source-root repo_dir/ --extractor-option python.skip_hidden_directories=true
+$CODEQL query run --database db-skipped query.ql > query-skipped.actual
+diff query-skipped.expected query-skipped.actual
+
+rm -rf db db-skipped
diff --git a/python/extractor/semmle/traverser.py b/python/extractor/semmle/traverser.py
index ad8bd38ae735..0945d8ace4bf 100644
--- a/python/extractor/semmle/traverser.py
+++ b/python/extractor/semmle/traverser.py
@@ -83,11 +83,10 @@ def _treewalk(self, path):
                 self.logger.debug("Ignoring %s (symlink)", fullpath)
                 continue
             if isdir(fullpath):
-                if fullpath in self.exclude_paths or is_hidden(fullpath):
-                    if is_hidden(fullpath):
-                        self.logger.debug("Ignoring %s (hidden)", fullpath)
-                    else:
-                        self.logger.debug("Ignoring %s (excluded)", fullpath)
+                if fullpath in self.exclude_paths:
+                    self.logger.debug("Ignoring %s (excluded)", fullpath)
+                elif is_hidden(fullpath):
+                    self.logger.debug("Ignoring %s (hidden)", fullpath)
                 else:
                     empty = True
                     for item in self._treewalk(fullpath):
@@ -101,7 +100,12 @@ def _treewalk(self, path):
                 self.logger.debug("Ignoring %s (filter)", fullpath)
 
 
-if os.name== 'nt':
+if os.environ.get("CODEQL_EXTRACTOR_PYTHON_OPTION_SKIP_HIDDEN_DIRECTORIES", "false") == "false":
+
+    def is_hidden(path):
+        return False
+
+elif os.name== 'nt':
     import ctypes
 
     def is_hidden(path):
diff --git a/python/ql/lib/change-notes/2025-04-30-extract-hidden-files-by-default.md b/python/ql/lib/change-notes/2025-04-30-extract-hidden-files-by-default.md
new file mode 100644
index 000000000000..96372513499f
--- /dev/null
+++ b/python/ql/lib/change-notes/2025-04-30-extract-hidden-files-by-default.md
@@ -0,0 +1,5 @@
+---
+category: minorAnalysis
+---
+
+- The Python extractor now extracts files in hidden directories by default. A new extractor option, `skip_hidden_directories` has been added as well. Setting it to `true` will make the extractor revert to the old behavior.
diff --git a/python/ql/test/2/extractor-tests/hidden/test.expected b/python/ql/test/2/extractor-tests/hidden/test.expected
index ca72363d8f02..21bd0dfb2dd9 100644
--- a/python/ql/test/2/extractor-tests/hidden/test.expected
+++ b/python/ql/test/2/extractor-tests/hidden/test.expected
@@ -1,3 +1,5 @@
+| .hidden/inner/test.py |
+| .hidden/module.py |
 | folder/module.py |
 | package |
 | package/__init__.py |
diff --git a/python/ql/test/extractor-tests/filter-option/Test.expected b/python/ql/test/extractor-tests/filter-option/Test.expected
index 7ade39a5998c..56b1e36c2a93 100644
--- a/python/ql/test/extractor-tests/filter-option/Test.expected
+++ b/python/ql/test/extractor-tests/filter-option/Test.expected
@@ -3,3 +3,4 @@
 | Module foo.bar |
 | Module foo.include_test |
 | Package foo |
+| Script hidden_foo.py |