diff --git a/devel/py-pybind11/Makefile b/devel/py-pybind11/Makefile
index a13d77c50b1a..eebeada778d6 100644
--- a/devel/py-pybind11/Makefile
+++ b/devel/py-pybind11/Makefile
@@ -1,22 +1,22 @@
 PORTNAME=	pybind11
-DISTVERSION=	3.0.1
+DISTVERSION=	3.0.3
 CATEGORIES=	devel python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Seamless interoperability between C++11 and Python
 WWW=		https://pybind11.readthedocs.io/en/stable/ \
 		https://github.com/pybind/pybind11
 
 LICENSE=	BSD3CLAUSE
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
 
 USES=		cmake:indirect python
 USE_PYTHON=	pep517 concurrent autoplist pytest
 
 NO_ARCH=	yes
 
 .include <bsd.port.mk>
diff --git a/devel/py-pybind11/distinfo b/devel/py-pybind11/distinfo
index dc2251267414..ae26d0d7130f 100644
--- a/devel/py-pybind11/distinfo
+++ b/devel/py-pybind11/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1760505164
-SHA256 (pybind11-3.0.1.tar.gz) = 9c0f40056a016da59bab516efb523089139fcc6f2ba7e4930854c61efb932051
-SIZE (pybind11-3.0.1.tar.gz) = 546914
+TIMESTAMP = 1776154105
+SHA256 (pybind11-3.0.3.tar.gz) = 00471cdb816882c484708bc5dde80815c8c11cea540ab2cc6410f5ddea434755
+SIZE (pybind11-3.0.3.tar.gz) = 587814
diff --git a/devel/py-pybind11/files/patch-CMakeLists.txt b/devel/py-pybind11/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..963ae9b6084b
--- /dev/null
+++ b/devel/py-pybind11/files/patch-CMakeLists.txt
@@ -0,0 +1,13 @@
+--- CMakeLists.txt.orig	2022-11-09 12:37:21 UTC
++++ CMakeLists.txt
+@@ -372,10 +357,6 @@ if(PYBIND11_INSTALL)
+     endif()
+   endif()
+   join_paths(includedir_for_pc_file "\${prefix}" "${CMAKE_INSTALL_INCLUDEDIR}")
+-  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11.pc.in"
+-                 "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc" @ONLY)
+-  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc"
+-          DESTINATION "${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig/")
+ 
+   # When building a wheel, include __init__.py's for modules
+   # (see https://github.com/pybind/pybind11/pull/5552)
diff --git a/devel/pybind11/Makefile b/devel/pybind11/Makefile
index e0a989feae80..f0ae92c8ba0a 100644
--- a/devel/pybind11/Makefile
+++ b/devel/pybind11/Makefile
@@ -1,28 +1,35 @@
 PORTNAME=	pybind11
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.0.1
+DISTVERSION=	3.0.3
 CATEGORIES=	devel python
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Seamless interoperability between C++11 and Python (cmake part)
 WWW=		https://pybind11.readthedocs.io/en/stable/ \
 		https://github.com/pybind/pybind11
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		cmake:testing compiler:c++11-lang python:build
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	pybind
 
 CMAKE_OFF=	PYBIND11_TEST
+CMAKE_ARGS=	-Dprefix_for_pc_file=${PREFIX}
 
 CMAKE_TESTING_ON=	PYBIND11_TEST # 6 tests are known to fail: https://github.com/pybind/pybind11/issues/4580
 CMAKE_TESTING_TARGET=	pytest
 
 NO_ARCH=	yes
 
-# tests of 3.0.1: 5 failed, 1253 passed, 20 skipped, 2 xfailed, 1 xpassed in 53.99s
+# tests as of 3.0.3: (see https://github.com/pybind/pybind11/issues/6037)
+# Results (39.99s):
+#          5 failed
+#       3884 passed
+#         26 skipped
+#          3 xfailed
+#          1 xpassed
 
 .include <bsd.port.mk>
diff --git a/devel/pybind11/distinfo b/devel/pybind11/distinfo
index 6153f18eacf0..71bdd57be5e8 100644
--- a/devel/pybind11/distinfo
+++ b/devel/pybind11/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1760503125
-SHA256 (pybind-pybind11-v3.0.1_GH0.tar.gz) = 741633da746b7c738bb71f1854f957b9da660bcd2dce68d71949037f0969d0ca
-SIZE (pybind-pybind11-v3.0.1_GH0.tar.gz) = 918227
+TIMESTAMP = 1776142309
+SHA256 (pybind-pybind11-v3.0.3_GH0.tar.gz) = 787459e1e186ee82001759508fefa408373eae8a076ffe0078b126c6f8f0ec5e
+SIZE (pybind-pybind11-v3.0.3_GH0.tar.gz) = 964282
diff --git a/devel/pybind11/files/patch-CMakeLists.txt b/devel/pybind11/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..b2e89bafe606
--- /dev/null
+++ b/devel/pybind11/files/patch-CMakeLists.txt
@@ -0,0 +1,11 @@
+--- CMakeLists.txt.orig	2026-04-14 05:04:19 UTC
++++ CMakeLists.txt
+@@ -375,7 +375,7 @@ if(PYBIND11_INSTALL)
+   configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11.pc.in"
+                  "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc" @ONLY)
+   install(FILES "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc"
+-          DESTINATION "${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig/")
++          DESTINATION "libdata/pkgconfig/")
+ 
+   # When building a wheel, include __init__.py's for modules
+   # (see https://github.com/pybind/pybind11/pull/5552)
diff --git a/devel/pybind11/files/patch-pybind11_commands.py b/devel/pybind11/files/patch-pybind11_commands.py
new file mode 100644
index 000000000000..6b1d3eb971f3
--- /dev/null
+++ b/devel/pybind11/files/patch-pybind11_commands.py
@@ -0,0 +1,11 @@
+--- pybind11/commands.py.orig	2026-04-14 05:00:01 UTC
++++ pybind11/commands.py
+@@ -31,7 +31,7 @@ def get_pkgconfig_dir() -> str:
+     """
+     Return the path to the pybind11 pkgconfig directory.
+     """
+-    pkgconfig_installed_path = os.path.join(DIR, "share", "pkgconfig")
++    pkgconfig_installed_path = os.path.join(DIR, "libdata", "pkgconfig")
+     if os.path.exists(pkgconfig_installed_path):
+         return pkgconfig_installed_path
+ 
diff --git a/devel/pybind11/pkg-plist b/devel/pybind11/pkg-plist
index f7f1c9dfdb14..02c7f0c45711 100644
--- a/devel/pybind11/pkg-plist
+++ b/devel/pybind11/pkg-plist
@@ -1,61 +1,63 @@
 include/pybind11/attr.h
 include/pybind11/buffer_info.h
 include/pybind11/cast.h
 include/pybind11/chrono.h
 include/pybind11/common.h
 include/pybind11/complex.h
 include/pybind11/conduit/README.txt
 include/pybind11/conduit/pybind11_conduit_v1.h
 include/pybind11/conduit/pybind11_platform_abi_id.h
 include/pybind11/conduit/wrap_include_python_h.h
 include/pybind11/critical_section.h
+include/pybind11/detail/argument_vector.h
 include/pybind11/detail/class.h
 include/pybind11/detail/common.h
 include/pybind11/detail/cpp_conduit.h
 include/pybind11/detail/descr.h
 include/pybind11/detail/dynamic_raw_ptr_cast_if_possible.h
 include/pybind11/detail/exception_translation.h
 include/pybind11/detail/function_record_pyobject.h
+include/pybind11/detail/holder_caster_foreign_helpers.h
 include/pybind11/detail/init.h
 include/pybind11/detail/internals.h
 include/pybind11/detail/native_enum_data.h
 include/pybind11/detail/pybind11_namespace_macros.h
 include/pybind11/detail/struct_smart_holder.h
 include/pybind11/detail/type_caster_base.h
 include/pybind11/detail/typeid.h
 include/pybind11/detail/using_smart_holder.h
 include/pybind11/detail/value_and_holder.h
 include/pybind11/eigen.h
 include/pybind11/eigen/common.h
 include/pybind11/eigen/matrix.h
 include/pybind11/eigen/tensor.h
 include/pybind11/embed.h
 include/pybind11/eval.h
 include/pybind11/functional.h
 include/pybind11/gil.h
 include/pybind11/gil_safe_call_once.h
 include/pybind11/gil_simple.h
 include/pybind11/iostream.h
 include/pybind11/native_enum.h
 include/pybind11/numpy.h
 include/pybind11/operators.h
 include/pybind11/options.h
 include/pybind11/pybind11.h
 include/pybind11/pytypes.h
 include/pybind11/stl.h
 include/pybind11/stl/filesystem.h
 include/pybind11/stl_bind.h
 include/pybind11/subinterpreter.h
 include/pybind11/trampoline_self_life_support.h
 include/pybind11/type_caster_pyobject_ptr.h
 include/pybind11/typing.h
 include/pybind11/warnings.h
+libdata/pkgconfig/pybind11.pc
 share/cmake/pybind11/FindPythonLibsNew.cmake
 share/cmake/pybind11/pybind11Common.cmake
 share/cmake/pybind11/pybind11Config.cmake
 share/cmake/pybind11/pybind11ConfigVersion.cmake
 share/cmake/pybind11/pybind11GuessPythonExtSuffix.cmake
 share/cmake/pybind11/pybind11NewTools.cmake
 share/cmake/pybind11/pybind11Targets.cmake
 share/cmake/pybind11/pybind11Tools.cmake
-share/pkgconfig/pybind11.pc