diff --git a/sci-ml/onnx/Manifest b/sci-ml/onnx/Manifest
index 9be6c0a2cbbc7..63363dcfb2f42 100644
--- a/sci-ml/onnx/Manifest
+++ b/sci-ml/onnx/Manifest
@@ -1,3 +1,2 @@
-DIST onnx-1.16.2.tar.gz 12429500 BLAKE2B 1541fd9e80e305bc0764d1f5d236a89a2f0d0d8819bd6f235c88d35985daf02f575854a537af193befbeab861b2fe6a9d5b8803975b8ae6a47d5d5a6dc28b661 SHA512 7a9a8493b9c007429629484156487395044506f34e72253640e626351cb623b390750b36af78a290786131e3dcac35f4eb269e8693b594b7ce7cb105bcf9318d
 DIST onnx-1.17.0.tar.gz 12475304 BLAKE2B 17e3cdd4bf101749ba841599d1b4e89ad80cfa3de6adabc10491f84ec928c385b1fe517e32657b24ca57d14780d51cc9a641860c06194cec082d9a9950004c8c SHA512 5a18e2b19ec9c18c8b115fb7e12ed98eddaa581c95f15c4dd420cd6c86e7caa04f9a393da589e76b89cf9b3544abd3749a8c77c2446782f37502eb74e9b1f661
 DIST onnx-1.18.0.tar.gz 12826788 BLAKE2B 7b48cf4017816c4ba926cc4bfcaf3b95d4630421e71e70f3f5ce47f2a9e152e1fa26ca1b407a198216fe777daf014546e35ce7ab06f47ddcebb5d71ee79e834c SHA512 2f38664947c8d1efc40620a7c1b1953d2aa4b0a37b67c4886b86e77c1d697363c26413413ddda8eabc545892fb1bcb43afc7e93e62f0901527524a2727e1ea8d
diff --git a/sci-ml/onnx/onnx-1.16.2-r1.ebuild b/sci-ml/onnx/onnx-1.16.2-r1.ebuild
deleted file mode 100644
index 555c3bac3c408..0000000000000
--- a/sci-ml/onnx/onnx-1.16.2-r1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 2022-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_EXT=1
-PYTHON_COMPAT=( python3_{10..12} )
-inherit distutils-r1 cmake
-
-DESCRIPTION="Open Neural Network Exchange (ONNX)"
-HOMEPAGE="https://github.com/onnx/onnx"
-SRC_URI="https://github.com/onnx/${PN}/archive/refs/tags/v${PV}.tar.gz
-	-> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~riscv"
-IUSE="disableStaticReg"
-RESTRICT="test"
-
-RDEPEND="
-	dev-python/protobuf[${PYTHON_USEDEP}]
-	dev-python/pybind11[${PYTHON_USEDEP}]
-	dev-libs/protobuf:=[protoc(+)]
-	dev-cpp/abseil-cpp:=
-"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	eapply "${FILESDIR}"/${PN}-1.15.0-hidden.patch
-	cmake_src_prepare
-	distutils-r1_src_prepare
-}
-
-python_configure_all()
-{
-	mycmakeargs=(
-		-DONNX_USE_PROTOBUF_SHARED_LIBS=ON
-		-DONNX_USE_LITE_PROTO=ON
-		-DONNX_BUILD_SHARED_LIBS=ON
-		-DONNX_DISABLE_STATIC_REGISTRATION=$(usex disableStaticReg ON OFF)
-	)
-	cmake_src_configure
-}
-
-src_configure() {
-	distutils-r1_src_configure
-}
-
-src_compile() {
-	mycmakeargs=(
-		-DONNX_USE_PROTOBUF_SHARED_LIBS=ON
-		-DONNX_USE_LITE_PROTO=ON
-		-DONNX_BUILD_SHARED_LIBS=ON
-		-DONNX_DISABLE_STATIC_REGISTRATION=$(usex disableStaticReg ON OFF)
-	)
-	CMAKE_ARGS="${mycmakeargs[@]}" distutils-r1_src_compile
-}
-
-python_compile_all() {
-	cmake_src_compile
-}
-
-python_install_all() {
-	cmake_src_install
-	distutils-r1_python_install_all
-}
-
-src_install() {
-	distutils-r1_src_install
-}