diff --git a/pkgs/tools/misc/yubikey-personalization-gui/default.nix b/pkgs/tools/misc/yubikey-personalization-gui/default.nix
deleted file mode 100644
index 1698737f2000..000000000000
--- a/pkgs/tools/misc/yubikey-personalization-gui/default.nix
+++ /dev/null
@@ -1,62 +0,0 @@
-{
-  stdenv,
-  lib,
-  fetchurl,
-  mkDerivation,
-  pkg-config,
-  qtbase,
-  qmake,
-  imagemagick,
-  libyubikey,
-  yubikey-personalization,
-}:
-
-mkDerivation rec {
-  pname = "yubikey-personalization-gui";
-  version = "3.1.25";
-
-  src = fetchurl {
-    url = "https://developers.yubico.com/yubikey-personalization-gui/Releases/yubikey-personalization-gui-${version}.tar.gz";
-    sha256 = "1knyv5yss8lhzaff6jpfqv12fjf1b8b21mfxzx3qi0hw4nl8n2v8";
-  };
-
-  nativeBuildInputs = [
-    pkg-config
-    qmake
-    imagemagick
-  ];
-  buildInputs = [
-    yubikey-personalization
-    qtbase
-    libyubikey
-  ];
-
-  installPhase = ''
-    install -D -m0755 build/release/yubikey-personalization-gui "$out/bin/yubikey-personalization-gui"
-    install -D -m0644 resources/lin/yubikey-personalization-gui.1 "$out/share/man/man1/yubikey-personalization-gui.1"
-
-    # Desktop files
-    install -D -m0644 resources/lin/yubikey-personalization-gui.desktop "$out/share/applications/yubikey-personalization-gui.desktop"
-
-    # Icons
-    install -D -m0644 resources/lin/yubikey-personalization-gui.xpm "$out/share/pixmaps/yubikey-personalization-gui.xpm"
-    install -D -m0644 resources/lin/yubikey-personalization-gui.png "$out/share/icons/hicolor/128x128/apps/yubikey-personalization-gui.png"
-    for SIZE in 16 24 32 48 64 96; do
-      # set modify/create for reproducible builds
-      convert -scale ''${SIZE} +set date:create +set date:modify \
-        resources/lin/yubikey-personalization-gui.png \
-        yubikey-personalization-gui.png
-
-      install -D -m0644 yubikey-personalization-gui.png "$out/share/icons/hicolor/''${SIZE}x''${SIZE}/apps/yubikey-personalization-gui.png"
-    done
-  '';
-
-  meta = with lib; {
-    broken = stdenv.hostPlatform.isDarwin;
-    homepage = "https://developers.yubico.com/yubikey-personalization-gui";
-    description = "QT based cross-platform utility designed to facilitate reconfiguration of the Yubikey";
-    license = licenses.bsd2;
-    platforms = platforms.unix;
-    mainProgram = "yubikey-personalization-gui";
-  };
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 096df1a9a019..ffc514177b0d 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -2107,6 +2107,7 @@ mapAliases {
   yandex-browser-corporate = throw "'yandex-browser-corporate' has been removed, as it was broken and unmaintained"; # Added 2025-04-17
   youtrack_2022_3 = throw "'youtrack_2022_3' has been removed as it was deprecated. Please update to the 'youtrack' package."; # Added 2024-10-17
   yrd = throw "'yrd' has been removed, as it was broken and unmaintained"; # added 2024-05-27
+  yubikey-personalization-gui = throw "'yubikey-personalization-gui' has been removed due to being archived upstream. Consider using 'yubioath-flutter' instead."; # Added 2025-06-07
   yuzu-ea = throw "yuzu-ea has been removed from nixpkgs, as it has been taken down upstream"; # Added 2024-03-04
   yuzu-early-access = throw "yuzu-early-access has been removed from nixpkgs, as it has been taken down upstream"; # Added 2024-03-04
   yuzu = throw "yuzu has been removed from nixpkgs, as it has been taken down upstream"; # Added 2024-03-04
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 339dc8a399fe..0e6d427e4b0d 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -9825,8 +9825,6 @@ with pkgs;
 
   yubikey-manager-qt = libsForQt5.callPackage ../tools/misc/yubikey-manager-qt { };
 
-  yubikey-personalization-gui = libsForQt5.callPackage ../tools/misc/yubikey-personalization-gui { };
-
   zlib = callPackage ../development/libraries/zlib {
     stdenv =
       # zlib is a dependency of xcbuild. Avoid an infinite recursion by using a bootstrap stdenv