diff --git a/pkgs/development/python-modules/apkit/default.nix b/pkgs/development/python-modules/apkit/default.nix
deleted file mode 100644
index ab07a00ddb46..000000000000
--- a/pkgs/development/python-modules/apkit/default.nix
+++ /dev/null
@@ -1,37 +0,0 @@
-{
-  lib,
-  buildPythonPackage,
-  fetchFromGitHub,
-  numpy,
-  scipy,
-}:
-
-buildPythonPackage {
-  pname = "apkit";
-  version = "unstable-2022-08-23";
-  format = "setuptools";
-
-  src = fetchFromGitHub {
-    owner = "hwp";
-    repo = "apkit";
-    rev = "40561738c3f585c590c3f0584bf2e3354eefbd48";
-    hash = "sha256-/pwoEKB6BD+wWy7QwPwwzSxGn+TAOaMzduOXyuoXC8g=";
-  };
-
-  propagatedBuildInputs = [
-    numpy
-    scipy
-  ];
-
-  pythonImportsCheck = [ "apkit" ];
-
-  # This package has no tests
-  doCheck = false;
-
-  meta = with lib; {
-    description = "Audio processing toolkit";
-    homepage = "https://github.com/hwp/apkit";
-    license = licenses.mit;
-    maintainers = with maintainers; [ GaetanLepage ];
-  };
-}
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index 42a22e0dbc57..f7fdd98b5baf 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -82,6 +82,7 @@ mapAliases ({
   ansible-navigator = throw "ansible-navigator has been promoted to a top-level attribute name: pkgs.ansible-navigator"; # Added 2024-08-07
   anyjson = throw "anyjson has been removed, it was using setuptools 2to3 translation feature, which has been removed in setuptools 58"; # added 2022-01-18
   apache-airflow = throw "apache-airflow has been moved out of pythonPackages and is available as a standalone package"; # added 2023-06-05
+  apkit = throw "apkit was removed because it is unmaintained upstream and different from apkit on PyPI"; # added 2025-09-13
   argon2_cffi = argon2-cffi; # added 2022-05-09
   arnparse = throw "arnparse has been removed because the upstream repository was archived in 2023"; # Added 2024-10-04
   APScheduler = apscheduler; # added 2023-02-19
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 0fc880511b5d..05ec16920fb7 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -789,8 +789,6 @@ self: super: with self; {
 
   apkinspector = callPackage ../development/python-modules/apkinspector { };
 
-  apkit = callPackage ../development/python-modules/apkit { };
-
   aplpy = callPackage ../development/python-modules/aplpy { };
 
   apollo-fpga = callPackage ../development/python-modules/apollo-fpga { };