diff --git a/pkgs/applications/virtualization/youki/fix-cargo-lock.patch b/pkgs/applications/virtualization/youki/fix-cargo-lock.patch
deleted file mode 100644
index 591047368347..000000000000
--- a/pkgs/applications/virtualization/youki/fix-cargo-lock.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff --git a/Cargo.lock b/Cargo.lock
-index ffbcdc33..62659a4d 100644
---- a/Cargo.lock
-+++ b/Cargo.lock
-@@ -1915,7 +1915,7 @@ checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c"
- 
- [[package]]
- name = "libcgroups"
--version = "0.3.2"
-+version = "0.3.3"
- dependencies = [
-  "anyhow",
-  "clap",
-@@ -1940,7 +1940,7 @@ dependencies = [
- 
- [[package]]
- name = "libcontainer"
--version = "0.3.2"
-+version = "0.3.3"
- dependencies = [
-  "anyhow",
-  "bitflags 2.5.0",
-@@ -1983,7 +1983,7 @@ dependencies = [
- 
- [[package]]
- name = "liboci-cli"
--version = "0.3.2"
-+version = "0.3.3"
- dependencies = [
-  "clap",
- ]
-@@ -3881,9 +3881,9 @@ dependencies = [
- 
- [[package]]
- name = "time"
--version = "0.3.34"
-+version = "0.3.36"
- source = "registry+https://github.com/rust-lang/crates.io-index"
--checksum = "c8248b6521bb14bc45b4067159b9b6ad792e2d6d754d6c41fb50e29fefe38749"
-+checksum = "5dfd88e563464686c916c7e46e623e520ddc6d79fa6641390f2e3fa86e83e885"
- dependencies = [
-  "deranged",
-  "itoa",
-@@ -3893,7 +3893,7 @@ dependencies = [
-  "powerfmt",
-  "serde",
-  "time-core",
-- "time-macros 0.2.17",
-+ "time-macros 0.2.18",
- ]
- 
- [[package]]
-@@ -3914,9 +3914,9 @@ dependencies = [
- 
- [[package]]
- name = "time-macros"
--version = "0.2.17"
-+version = "0.2.18"
- source = "registry+https://github.com/rust-lang/crates.io-index"
--checksum = "7ba3a3ef41e6672a2f0f001392bb5dcd3ff0a9992d618ca761a11c3121547774"
-+checksum = "3f252a68540fde3a3877aeea552b832b40ab9a69e318efd078774a01ddee1ccf"
- dependencies = [
-  "num-conv",
-  "time-core",
-@@ -4287,7 +4287,7 @@ dependencies = [
-  "anyhow",
-  "cfg-if",
-  "rustversion",
-- "time 0.3.34",
-+ "time 0.3.36",
- ]
- 
- [[package]]
-@@ -5678,7 +5678,7 @@ dependencies = [
- 
- [[package]]
- name = "youki"
--version = "0.3.2"
-+version = "0.3.3"
- dependencies = [
-  "anyhow",
-  "caps",
diff --git a/pkgs/applications/virtualization/youki/default.nix b/pkgs/by-name/yo/youki/package.nix
similarity index 85%
rename from pkgs/applications/virtualization/youki/default.nix
rename to pkgs/by-name/yo/youki/package.nix
index 01e400805669..8e5d57ae7a36 100644
--- a/pkgs/applications/virtualization/youki/default.nix
+++ b/pkgs/by-name/yo/youki/package.nix
@@ -12,17 +12,15 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "youki";
-  version = "0.3.3";
+  version = "0.4.0";
 
   src = fetchFromGitHub {
     owner = "containers";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-lOt+bi9JbHLRUFiSoIfgNH2f9LXcrKk7vSz8fXLFDJE=";
+    hash = "sha256-dkVnNtBfvjf47p1N5/syHqjlDVnbKRDqNJ98ym5B+mg=";
   };
 
-  cargoPatches = [ ./fix-cargo-lock.patch ];
-
   nativeBuildInputs = [
     pkg-config
     installShellFiles
@@ -50,7 +48,7 @@ rustPlatform.buildRustPackage rec {
     "youki"
   ];
 
-  cargoHash = "sha256-bbKuycv747NKtxhnakASRtlkPqT2Ry6g0z4Zi1EuNzQ=";
+  cargoHash = "sha256-Nv1LAkWYwWb0Izvd7UlKU4wx3vVkmO9Rcpt6AuTwObU=";
 
   meta = with lib; {
     description = "Container runtime written in Rust";
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 9645c6d7550f..73e489f80196 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -34839,8 +34839,6 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) CoreFoundation Security AppKit;
   };
 
-  youki = callPackage ../applications/virtualization/youki { };
-
   yt-dlp-light = yt-dlp.override {
     atomicparsleySupport = false;
     ffmpegSupport = false;