diff --git a/pkgs/development/python-modules/configargparse/default.nix b/pkgs/development/python-modules/configargparse/default.nix
index ff89b6a2a52c..8f9a2bee6135 100644
--- a/pkgs/development/python-modules/configargparse/default.nix
+++ b/pkgs/development/python-modules/configargparse/default.nix
@@ -5,6 +5,7 @@
   mock,
   pytestCheckHook,
   pyyaml,
+  pythonAtLeast,
   pythonOlder,
 }:
 
@@ -22,6 +23,11 @@ buildPythonPackage rec {
     hash = "sha256-m77MY0IZ1AJkd4/Y7ltApvdF9y17Lgn92WZPYTCU9tA=";
   };
 
+  patches = [
+    # https://github.com/bw2/ConfigArgParse/pull/295
+    ./python3.13-compat.patch
+  ];
+
   optional-dependencies = {
     yaml = [ pyyaml ];
   };
@@ -29,7 +35,12 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     pytestCheckHook
     mock
-  ] ++ lib.flatten (builtins.attrValues optional-dependencies);
+  ] ++ lib.flatten (lib.attrValues optional-dependencies);
+
+  disabledTests = lib.optionals (pythonAtLeast "3.13") [
+    # regex mismatch
+    "testMutuallyExclusiveArgs"
+  ];
 
   pythonImportsCheck = [ "configargparse" ];
 
diff --git a/pkgs/development/python-modules/configargparse/python3.13-compat.patch b/pkgs/development/python-modules/configargparse/python3.13-compat.patch
new file mode 100644
index 000000000000..a079f37a18e6
--- /dev/null
+++ b/pkgs/development/python-modules/configargparse/python3.13-compat.patch
@@ -0,0 +1,112 @@
+From c6a974211f1a13d492bb807ff6d07cefcc948a87 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
+Date: Fri, 12 Jul 2024 08:15:40 +0200
+Subject: [PATCH 1/2] update test expectations for Python 3.13
+
+Python 3.13 no longer repeats the placeholder for options with multiple
+aliases in the help message.  For example, rather than:
+
+    -c CONFIG_FILE, --config CONFIG_FILE
+
+it now outputs:
+
+    -c, --config CONFIG_FILE
+
+Update the regular expressions to account for both possibilities.
+
+Fixes #294
+---
+ tests/test_configargparse.py | 24 ++++++++++++------------
+ 1 file changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/tests/test_configargparse.py b/tests/test_configargparse.py
+index 288e082..e325afd 100644
+--- a/tests/test_configargparse.py
++++ b/tests/test_configargparse.py
+@@ -271,9 +271,9 @@ def testBasicCase2(self, use_groups=False):
+                 '  -h, --help \\s+ show this help message and exit\n'
+                 '  --genome GENOME \\s+ Path to genome file\n'
+                 '  -v\n'
+-                '  -g MY_CFG_FILE, --my-cfg-file MY_CFG_FILE\n'
+-                '  -d DBSNP, --dbsnp DBSNP\\s+\\[env var: DBSNP_PATH\\]\n'
+-                '  -f FRMT, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n\n'%OPTIONAL_ARGS_STRING +
++                '  -g( MY_CFG_FILE)?, --my-cfg-file MY_CFG_FILE\n'
++                '  -d( DBSNP)?, --dbsnp DBSNP\\s+\\[env var: DBSNP_PATH\\]\n'
++                '  -f( FRMT)?, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n\n'%OPTIONAL_ARGS_STRING +
+                 7*r'(.+\s*)')
+         else:
+             self.assertRegex(self.format_help(),
+@@ -286,10 +286,10 @@ def testBasicCase2(self, use_groups=False):
+                 'g1:\n'
+                 '  --genome GENOME \\s+ Path to genome file\n'
+                 '  -v\n'
+-                '  -g MY_CFG_FILE, --my-cfg-file MY_CFG_FILE\n\n'
++                '  -g( MY_CFG_FILE)?, --my-cfg-file MY_CFG_FILE\n\n'
+                 'g2:\n'
+-                '  -d DBSNP, --dbsnp DBSNP\\s+\\[env var: DBSNP_PATH\\]\n'
+-                '  -f FRMT, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n\n'%OPTIONAL_ARGS_STRING +
++                '  -d( DBSNP)?, --dbsnp DBSNP\\s+\\[env var: DBSNP_PATH\\]\n'
++                '  -f( FRMT)?, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n\n'%OPTIONAL_ARGS_STRING +
+                 7*r'(.+\s*)')
+ 
+         self.assertParseArgsRaises("invalid choice: 'ZZZ'",
+@@ -387,9 +387,9 @@ def testMutuallyExclusiveArgs(self):
+             ' \\s*-f2 TYPE2_CFG_FILE\\)\\s+\\(-f FRMT \\| -b\\)\n\n'
+             '%s:\n'
+             '  -h, --help            show this help message and exit\n'
+-            '  -f1 TYPE1_CFG_FILE, --type1-cfg-file TYPE1_CFG_FILE\n'
+-            '  -f2 TYPE2_CFG_FILE, --type2-cfg-file TYPE2_CFG_FILE\n'
+-            '  -f FRMT, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n'
++            '  -f1( TYPE1_CFG_FILE)?, --type1-cfg-file TYPE1_CFG_FILE\n'
++            '  -f2( TYPE2_CFG_FILE)?, --type2-cfg-file TYPE2_CFG_FILE\n'
++            '  -f( FRMT)?, --format FRMT\\s+\\[env var: OUTPUT_FORMAT\\]\n'
+             '  -b, --bam\\s+\\[env var: BAM_FORMAT\\]\n\n'
+             'group1:\n'
+             '  --genome GENOME       Path to genome file\n'
+@@ -875,7 +875,7 @@ def testConstructor_ConfigFileArgs(self):
+             'usage: .* \\[-h\\] -c CONFIG_FILE --genome GENOME\n\n'
+             '%s:\n'
+             '  -h, --help\\s+ show this help message and exit\n'
+-            '  -c CONFIG_FILE, --config CONFIG_FILE\\s+ my config file\n'
++            '  -c( CONFIG_FILE)?, --config CONFIG_FILE\\s+ my config file\n'
+             '  --genome GENOME\\s+ Path to genome file\n\n'%OPTIONAL_ARGS_STRING +
+             5*r'(.+\s*)')
+ 
+@@ -935,8 +935,8 @@ def test_FormatHelp(self):
+             r'\[-w CONFIG_OUTPUT_PATH\]\s* --arg1\s+ARG1\s*\[--flag\]\s*'
+             '%s:\\s*'
+             '-h, --help \\s* show this help message and exit '
+-            r'-c CONFIG_FILE, --config CONFIG_FILE\s+my config file '
+-            r'-w CONFIG_OUTPUT_PATH, --write-config CONFIG_OUTPUT_PATH takes '
++            r'-c( CONFIG_FILE)?, --config CONFIG_FILE\s+my config file '
++            r'-w( CONFIG_OUTPUT_PATH)?, --write-config CONFIG_OUTPUT_PATH takes '
+             r'the current command line args and writes them '
+             r'out to a config file at the given path, then exits '
+             r'--arg1 ARG1 Arg1 help text '
+
+From 5e9f442374bc6d9707a43df13aaff684dff6b535 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
+Date: Fri, 12 Jul 2024 08:25:30 +0200
+Subject: [PATCH 2/2] skip exit_on_error* tests to fix 3.13 test failures
+
+Skip `exit_on_error*` tests from `test.test_argparse` to avoid test
+failures on Python 3.13.  The `exit_on_error=False` semantics
+is not supported by ConfigArgParse at the moment.
+---
+ tests/test_configargparse.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/tests/test_configargparse.py b/tests/test_configargparse.py
+index e325afd..9718d86 100644
+--- a/tests/test_configargparse.py
++++ b/tests/test_configargparse.py
+@@ -1533,7 +1533,8 @@ def testYAMLConfigFileParser_w_ArgumentParser_parsed_values(self):
+     test_argparse_source_code = test_argparse_source_code.replace(
+         'argparse.ArgumentParser', 'configargparse.ArgumentParser').replace(
+         'TestHelpFormattingMetaclass', '_TestHelpFormattingMetaclass').replace(
+-        'test_main', '_test_main')
++        'test_main', '_test_main').replace(
++        'test_exit_on_error', '_test_exit_on_error')
+ 
+     # pytest tries to collect tests from TestHelpFormattingMetaclass, and
+     # test_main, and raises a warning when it finds it's not a test class