diff --git a/app-text/doxygen/Manifest b/app-text/doxygen/Manifest
index 3bdee49c808ef..626692da9acb6 100644
--- a/app-text/doxygen/Manifest
+++ b/app-text/doxygen/Manifest
@@ -1,3 +1,4 @@
 DIST doxygen-1.13.2.src.tar.gz 8512178 BLAKE2B d1a5051b49924580cf2e4f58df12da6ff6f9f02490957b1a1562a7587763ab32bac11b0c7d3456d6fee48e7284ee8a265e90d1862a40af2c6deb9d1ebdef72e9 SHA512 7b6b3285706e10c0b27230503b83cc669aec83ebc3ef9cc1087d5e36118fd726a5368d567dd553ba01acf4d739cdbb41c5e66af4541fc8e51effbbdaa241c812
 DIST doxygen-1.14.0.src.tar.gz 8681251 BLAKE2B 7de83955033348bea7ecb8d4b2b106192496ffcd062b5fff7f7cfe1f8d25b372d661608f92a5fdfc14489b7343fd19819dd1c86de0d936136714a4f1edd89595 SHA512 b042f7f731cd17bea55f7393dd90433f49fa296a61054950c2e1457ff1d57e218706cbc4f5248f42c2242bf1acccd91e88cf545ca394a31a4d2d8b7f5954baa9
 DIST doxygen-1.15.0.src.tar.gz 9203196 BLAKE2B 461d65ad4a18488cd8c89fc1268bb57e31964cac431acfca8c5ad3947d70f47af441579cad6b54945b337c57fb8ad0e219f804a1d8cfdda3b2595fb9803e7605 SHA512 e53cc8da6cf1fe3ca3b3637647ed6afa28365351eac81d010f6691d939df5e449b3d898a6f695dd850d12659dfd7018fc864071b30fbca5dd196dc094ec4371e
+DIST doxygen-1.16.1.src.tar.gz 8962809 BLAKE2B 534064d1207d5e44430fa1bde14f0b4dd0afd56e7bafd7b3866d2037dd87063099fe32c2fee652a6508298fa8bba610c0198601bca2a42743d34ad1db83051cc SHA512 16c348e2943319e38fe2c0c3539c9b481c613a094f59c4fe16251bf7c62fa77cd979cff97507296721dd7f6cd9c1bd2bda13ab1740a13cef8fda31601878d09d
diff --git a/app-text/doxygen/doxygen-1.16.1.ebuild b/app-text/doxygen/doxygen-1.16.1.ebuild
new file mode 100644
index 0000000000000..3d3d51c69616f
--- /dev/null
+++ b/app-text/doxygen/doxygen-1.16.1.ebuild
@@ -0,0 +1,143 @@
+# Copyright 1999-2026 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+LLVM_COMPAT=( 18 19 20 21 )
+LLVM_OPTIONAL=1
+PYTHON_COMPAT=( python3_{11..14} )
+PYTHON_REQ_USE="xml(+)"
+
+inherit cmake flag-o-matic llvm-r1 python-any-r1
+
+DESCRIPTION="Documentation system for most programming languages"
+HOMEPAGE="https://www.doxygen.nl/"
+
+if [[ ${PV} == *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/doxygen/doxygen.git"
+else
+	SRC_URI="https://doxygen.nl/files/${P}.src.tar.gz"
+	SRC_URI+=" https://downloads.sourceforge.net/doxygen/rel-${PV}/${P}.src.tar.gz"
+	KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~loong ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~x64-macos ~x64-solaris"
+fi
+
+# GPL-2 also for bundled libmscgen
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="clang debug doc dot doxysearch gui test"
+# - We need TeX for tests, bug #765472
+# - We keep the odd construct of noop USE=test because of
+#   the special relationship b/t RESTRICT & USE for tests.
+#   Also, it's a hint which avoids tests being silently skipped during arch testing.
+REQUIRED_USE="clang? ( ${LLVM_REQUIRED_USE} ) test? ( doc )"
+RESTRICT="!test? ( test )"
+
+BDEPEND="
+	app-alternatives/yacc
+	app-alternatives/lex
+	${PYTHON_DEPS}
+"
+RDEPEND="
+	app-text/ghostscript-gpl
+	dev-db/sqlite:3
+	dev-lang/perl
+	dev-libs/libfmt:=
+	dev-libs/spdlog:=
+	virtual/libiconv
+	clang? (
+		$(llvm_gen_dep '
+			llvm-core/clang:${LLVM_SLOT}=
+			llvm-core/llvm:${LLVM_SLOT}=
+		')
+	)
+	dot? (
+		media-gfx/graphviz[freetype(+)]
+	)
+	doc? (
+		dev-texlive/texlive-bibtexextra
+		dev-texlive/texlive-fontsextra
+		dev-texlive/texlive-fontutils
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		dev-texlive/texlive-plaingeneric
+	)
+	doxysearch? ( dev-libs/xapian:= )
+	gui? (
+		dev-qt/qtbase:6[gui,widgets,xml]
+		dev-qt/qtsvg:6
+	)
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-1.15.0-link_with_pthread.patch"
+	"${FILESDIR}/${PN}-1.16.1-suppress-unused-option-libcxx.patch"
+)
+
+DOCS=( LANGUAGE.HOWTO README.md )
+
+pkg_setup() {
+	use clang && llvm-r1_pkg_setup
+	python-any-r1_pkg_setup
+}
+
+src_prepare() {
+	cmake_src_prepare
+
+	# Call dot with -Teps instead of -Tps for EPS generation - bug #282150
+	sed -i -e '/addJob("ps"/ s/"ps"/"eps"/g' src/dot.cpp || die
+
+	# fix pdf doc
+	sed -i.orig -e "s:g_kowal:g kowal:" \
+		doc/maintainers.txt || die
+
+	if is-flagq "-O3" ; then
+		# TODO: Investigate this and report a bug accordingly...
+		ewarn "Compiling with -O3 is known to produce incorrectly"
+		ewarn "optimized code which breaks doxygen. Using -O2 instead."
+		replace-flags "-O3" "-O2"
+	fi
+}
+
+src_configure() {
+	# Very slow to compile, bug #920092
+	filter-flags -fipa-pta
+	# -Wodr warnings, see bug #854357 and https://github.com/doxygen/doxygen/issues/9287
+	filter-lto
+
+	local mycmakeargs=(
+		-Duse_libclang=$(usex clang)
+		# Let the user choose instead, see also bug #822615
+		-Duse_libc++=OFF
+		-Dbuild_doc=$(usex doc)
+		-Dbuild_search=$(usex doxysearch)
+		-Dbuild_wizard=$(usex gui)
+		-Dforce_qt=Qt6
+		-Duse_sys_fmt=ON
+		-Duse_sys_spdlog=ON
+		-Duse_sys_sqlite3=ON
+		-DBUILD_SHARED_LIBS=OFF
+		-DGIT_EXECUTABLE="false"
+
+		# Noisy and irrelevant downstream
+		-Wno-dev
+	)
+
+	use doc && mycmakeargs+=(
+		-DDOC_INSTALL_DIR="share/doc/${P}"
+	)
+
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+
+	if use doc; then
+		export VARTEXFONTS="${T}/fonts" # bug #564944
+
+		# -j1 for bug #770070
+		cmake_src_compile docs -j1
+	fi
+}
diff --git a/app-text/doxygen/files/doxygen-1.16.1-suppress-unused-option-libcxx.patch b/app-text/doxygen/files/doxygen-1.16.1-suppress-unused-option-libcxx.patch
new file mode 100644
index 0000000000000..67fac81af52f1
--- /dev/null
+++ b/app-text/doxygen/files/doxygen-1.16.1-suppress-unused-option-libcxx.patch
@@ -0,0 +1,16 @@
+Always expose the use_libc++ option. It's only useful for Clang but cmake.class
+tries to find when we've used CMake options which are unused/unknown and this
+triggers it for GCC builds if we set -Duse_libc++=OFF.
+
+So, always expose the option so we can turn it off without a warning.
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -22,7 +22,7 @@ option(build_parse     "Parses source code and dumps the dependencies between th
+ option(build_search    "Build external search tools (doxysearch and doxyindexer)" OFF)
+ option(build_doc       "Build user manual (HTML and PDF)" OFF)
+ option(build_doc_chm   "Build user manual (CHM)" OFF)
+-if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
++if(TRUE)
+   option(use_libc++  "Use libc++ as C++ standard library." ON)
+ endif()
+ option(use_libclang    "Add support for libclang parsing." OFF)