diff --git a/pkgs/development/libraries/openbabel/2.nix b/pkgs/development/libraries/openbabel/2.nix
deleted file mode 100644
index 90b27abf02d6..000000000000
--- a/pkgs/development/libraries/openbabel/2.nix
+++ /dev/null
@@ -1,62 +0,0 @@
-{
-  stdenv,
-  lib,
-  fetchFromGitHub,
-  fetchpatch,
-  cmake,
-  zlib,
-  libxml2,
-  eigen,
-  python3,
-  cairo,
-  pcre,
-  pkg-config,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "openbabel";
-  version = "2.4.1";
-
-  src = fetchFromGitHub {
-    owner = "openbabel";
-    repo = "openbabel";
-    rev = "openbabel-${lib.replaceStrings [ "." ] [ "-" ] version}";
-    sha256 = "sha256-+pXsWMzex7rB1mm6dnTHzAcyw9jImgx1OZuLeCvbeJ0=";
-  };
-
-  patches = [
-    # ARM / AArch64 fixes.
-    (fetchpatch {
-      url = "https://github.com/openbabel/openbabel/commit/ee11c98a655296550710db1207b294f00e168216.patch";
-      sha256 = "0wjqjrkr4pfirzzicdvlyr591vppydk572ix28jd2sagnfnf566g";
-    })
-  ];
-
-  postPatch = ''
-    sed '1i#include <ctime>' -i include/openbabel/obutil.h # gcc12
-  '';
-
-  buildInputs = [
-    zlib
-    libxml2
-    eigen
-    python3
-    cairo
-    pcre
-  ];
-
-  cmakeFlags = [ "-DCMAKE_CXX_STANDARD=14" ];
-
-  nativeBuildInputs = [
-    cmake
-    pkg-config
-  ];
-
-  meta = with lib; {
-    description = "Toolbox designed to speak the many languages of chemical data";
-    homepage = "http://openbabel.org";
-    platforms = platforms.all;
-    maintainers = with maintainers; [ danielbarter ];
-    license = licenses.gpl2Plus;
-  };
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 5cbd55605913..e5daae223997 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1859,6 +1859,7 @@ mapAliases {
   onevpl-intel-gpu = lib.warnOnInstantiate "onevpl-intel-gpu has been renamed to vpl-gpu-rt" vpl-gpu-rt; # Added 2024-06-04
   openai-triton-llvm = triton-llvm; # added 2024-07-18
   openai-whisper-cpp = whisper-cpp; # Added 2024-12-13
+  openbabel2 = throw "openbabel2 has been removed, as it was unused and unmaintained upstream; please use openbabel"; # Added 2025-09-17
   opencv2 = throw "opencv2 has been removed as it is obsolete and was not used by any other package; please migrate to OpenCV 4"; # Added 2024-08-20
   opencv3 = throw "opencv3 has been removed as it is obsolete and was not used by any other package; please migrate to OpenCV 4"; # Added 2024-08-20
   openafs_1_8 = openafs; # Added 2022-08-22
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index cdfb419f5279..8abbf6ead7fd 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -8491,8 +8491,6 @@ with pkgs;
 
   openbabel = openbabel3;
 
-  openbabel2 = callPackage ../development/libraries/openbabel/2.nix { };
-
   openbabel3 = callPackage ../development/libraries/openbabel { };
 
   opencascade-occt_7_6 = opencascade-occt.overrideAttrs rec {