diff --git a/pkgs/by-name/ch/chemtool/package.nix b/pkgs/by-name/ch/chemtool/package.nix
deleted file mode 100644
index 344b1d66150b..000000000000
--- a/pkgs/by-name/ch/chemtool/package.nix
+++ /dev/null
@@ -1,61 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchurl,
-  pkg-config,
-  libx11,
-  gtk2,
-  fig2dev,
-  wrapGAppsHook3,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "chemtool";
-  version = "1.6.14";
-
-  src = fetchurl {
-    url = "http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool-${finalAttrs.version}.tar.gz";
-    sha256 = "hhYaBGE4azNKX/sXzfCUpJGUGIRngnL0V0mBNRTdr8s=";
-  };
-
-  nativeBuildInputs = [
-    pkg-config
-    wrapGAppsHook3
-  ];
-  buildInputs = [
-    libx11
-    gtk2
-    fig2dev
-  ];
-
-  # Workaround build on -fno-common toolchains like upstream gcc-10.
-  # Otherwise built fails as:
-  #   ld: inout.o:/build/chemtool-1.6.14/ct1.h:279: multiple definition of
-  #     `outtype'; draw.o:/build/chemtool-1.6.14/ct1.h:279: first defined here
-  env.NIX_CFLAGS_COMPILE = "-fcommon";
-
-  preFixup = ''
-    gappsWrapperArgs+=(--prefix PATH : "${lib.makeBinPath [ fig2dev ]}")
-  '';
-
-  meta = {
-    homepage = "http://ruby.chemie.uni-freiburg.de/~martin/chemtool/";
-    description = "Draw chemical structures";
-    longDescription = ''
-      Chemtool is a program for drawing organic molecules. It runs under the X
-      Window System using the GTK widget set.
-
-      Most operations in chemtool can be accomplished using the mouse - the
-      first (usually the left) button is used to select or place things, the
-      middle button modifies properties (e.g. reverses the direction of a bond),
-      and the right button is used to delete objects.
-
-      The program offers essentially unlimited undo/redo, two text fonts plus
-      symbols, seven colors, drawing at several zoom scales, and square and
-      hexagonal backdrop grids for easier alignment.
-    '';
-    license = lib.licenses.mit;
-    maintainers = [ ];
-    platforms = lib.platforms.linux;
-  };
-})
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 4e519a3476e4..c2c07565d362 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -475,6 +475,7 @@ mapAliases {
   check_systemd = throw "'check_systemd' has been renamed to/replaced by 'nagiosPlugins.check_systemd'"; # Converted to throw 2025-10-27
   check_zfs = throw "'check_zfs' has been renamed to/replaced by 'nagiosPlugins.check_zfs'"; # Converted to throw 2025-10-27
   checkSSLCert = throw "'checkSSLCert' has been renamed to/replaced by 'nagiosPlugins.check_ssl_cert'"; # Converted to throw 2025-10-27
+  chemtool = throw "'chemtool' has been removed, as it is unmaintained upstream and depends on GTK 2. Consider using 'avogadro2' instead."; # Added 2026-05-22
   chiaki4deck = throw "'chiaki4deck' has been renamed to/replaced by 'chiaki-ng'"; # Converted to throw 2025-10-27
   chit = throw "'chit' has been removed from nixpkgs because it was unmaintained upstream and used insecure dependencies"; # Added 2025-11-28
   chkrootkit = throw "chkrootkit has been removed as it is unmaintained and archived upstream and didn't even work on NixOS"; # Added 2025-09-12