diff --git a/pkgs/development/python-modules/ruffus/default.nix b/pkgs/development/python-modules/ruffus/default.nix
deleted file mode 100644
index c21d1fcbd0d9..000000000000
--- a/pkgs/development/python-modules/ruffus/default.nix
+++ /dev/null
@@ -1,56 +0,0 @@
-{
-  gevent,
-  buildPythonPackage,
-  fetchFromGitHub,
-  hostname,
-  pytest,
-  pythonAtLeast,
-  lib,
-  stdenv,
-}:
-
-buildPythonPackage rec {
-  pname = "ruffus";
-  version = "2.8.4";
-  format = "setuptools";
-
-  src = fetchFromGitHub {
-    owner = "cgat-developers";
-    repo = "ruffus";
-    rev = "v${version}";
-    sha256 = "0fnzpchwwqsy5h18fs0n90s51w25n0dx0l74j0ka6lvhjl5sxn4c";
-  };
-
-  propagatedBuildInputs = [ gevent ];
-
-  nativeCheckInputs = [
-    hostname
-    pytest
-  ];
-
-  # tests very flaky & hang often on darwin
-  doCheck = !stdenv.hostPlatform.isDarwin;
-  checkPhase =
-    # https://docs.python.org/3/whatsnew/3.13.html#re
-    lib.optionalString (pythonAtLeast "3.13") ''
-      substituteInPlace ruffus/test/test_ruffus_utility.py \
-        --replace-fail re.error re.PatternError
-    ''
-    # test files do indeed need to be executed separately
-    + ''
-      pushd ruffus/test
-      rm test_with_logger.py  # spawns 500 processes
-      for f in test_*.py ; do
-        HOME=$TMPDIR pytest -v --disable-warnings $f
-      done
-      popd
-    '';
-  pythonImportsCheck = [ "ruffus" ];
-
-  meta = {
-    description = "Light-weight Python Computational Pipeline Management";
-    homepage = "http://www.ruffus.org.uk";
-    license = lib.licenses.mit;
-    maintainers = [ ];
-  };
-}
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index 0e0f3767e221..4e908bb2838f 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -499,6 +499,7 @@ mapAliases {
   ruamel_base = throw "'ruamel_base' has been renamed to/replaced by 'ruamel-base'"; # Converted to throw 2025-10-29
   ruamel_yaml = throw "'ruamel_yaml' has been renamed to/replaced by 'ruamel-yaml'"; # Converted to throw 2025-10-29
   ruamel_yaml_clib = throw "'ruamel_yaml_clib' has been renamed to/replaced by 'ruamel-yaml-clib'"; # Converted to throw 2025-10-29
+  ruffus = throw "'ruffus' has been removed as it was unmaintained and abandoned upstream"; # Added 2026-03-21
   sapi-python-client = throw "'sapi-python-client' has been renamed to/replaced by 'kbcstorage'"; # Converted to throw 2025-10-29
   schemainspect = throw "schemainspect has been removed because it has transitively been marked broken since May 2024, and is unmaintained upstream."; # Added 2025-10-11
   scikitimage = throw "'scikitimage' has been renamed to/replaced by 'scikit-image'"; # Converted to throw 2025-10-29
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 27c448e0e2a7..6e02a989331c 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -17089,8 +17089,6 @@ self: super: with self; {
 
   ruff-api = callPackage ../development/python-modules/ruff-api { };
 
-  ruffus = callPackage ../development/python-modules/ruffus { };
-
   rules = callPackage ../development/python-modules/rules { };
 
   rumps = callPackage ../development/python-modules/rumps { };