diff --git a/science/phonopy/Makefile b/science/phonopy/Makefile
index 79dae27c15f8..15241ef5732b 100644
--- a/science/phonopy/Makefile
+++ b/science/phonopy/Makefile
@@ -1,26 +1,26 @@
 PORTNAME=	phonopy
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.38.0
+DISTVERSION=	2.41.2
 CATEGORIES=	science python
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Package for phonon calculations at harmonic and quasi-harmonic levels
 WWW=		https://phonopy.github.io/phonopy/ \
 		https://github.com/phonopy/phonopy
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		cmake
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
 
 CMAKE_ON=	PHONOPY PHONOPY_LIBS BUILD_SHARED_LIBS
 
 PLIST_FILES=	include/phonopy.h \
 		lib/libphonopy_libs.so \
 		lib/libphonopy_libs.so.1 \
 		lib/libphonopy_libs.so.${DISTVERSION}
 
 .include <bsd.port.mk>
diff --git a/science/phonopy/distinfo b/science/phonopy/distinfo
index fd9b3ed7de36..242c3100549a 100644
--- a/science/phonopy/distinfo
+++ b/science/phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1741068945
-SHA256 (phonopy-phonopy-v2.38.0_GH0.tar.gz) = e98c2b63f5cd847aa2efe6aa714ed1e656a3a2dba6f167830fc3149ee6bef4f1
-SIZE (phonopy-phonopy-v2.38.0_GH0.tar.gz) = 7712107
+TIMESTAMP = 1752739755
+SHA256 (phonopy-phonopy-v2.41.2_GH0.tar.gz) = e78053c18dc6550bab6533b78704162c8d5bf0207ffcf3d61d636c0a4f9cbb33
+SIZE (phonopy-phonopy-v2.41.2_GH0.tar.gz) = 7717842
diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile
index bb9438585200..43101eaa6ecd 100644
--- a/science/py-phonopy/Makefile
+++ b/science/py-phonopy/Makefile
@@ -1,41 +1,41 @@
 PORTNAME=	phonopy
-DISTVERSION=	2.38.0
+DISTVERSION=	2.41.2
 CATEGORIES=	science python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Package for phonon calculations at harmonic and quasi-harmonic levels
 WWW=		https://phonopy.github.io/phonopy/ \
 		https://github.com/phonopy/phonopy
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	cmake:devel/cmake-core \
 		${PYTHON_PKGNAMEPREFIX}nanobind>0:devel/py-nanobind@${PY_FLAVOR} \
 		${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \
 		${PY_SETUPTOOLS} \
 		${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR}
 RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}h5py>=3.0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.2:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}spglib>=2.3:science/py-spglib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}symfc>=1.1.6:science/py-symfc@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pyyaml>=5.3:devel/py-pyyaml@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hiphive>0:science/py-hiphive@${PY_FLAVOR}
 
 USES=		python
 USE_PYTHON=	pep517 cython autoplist pytest
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 TEST_WRKSRC=	${WRKSRC}/test
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/phonopy/_phonopy${PYTHON_TAG}.so
 
-# tests as of 2.37.0: 3 failed, 270 passed, 4 skipped, 4 warnings, 5 errors in 1448.81s (0:24:08) (failures are likely in science/py-symfc with -9999 error)
+# tests as of 2.41.2: 6 failed, 159 passed, 5 skipped, 21 warnings, 130 errors in 502.46s (0:08:22) (failures are likely in science/py-symfc with -9999 error)
 
 .include <bsd.port.mk>
diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo
index 73eee825c0b9..740077509ed3 100644
--- a/science/py-phonopy/distinfo
+++ b/science/py-phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1741068971
-SHA256 (phonopy-2.38.0.tar.gz) = f2c285affe76b45fcef59d6323c7da727bbcfcdf25e0684cbdae46fccdcf40cf
-SIZE (phonopy-2.38.0.tar.gz) = 4712135
+TIMESTAMP = 1752739793
+SHA256 (phonopy-2.41.2.tar.gz) = 850f1c298c1013c641ecbc94cd181cef3261b213655859d4bd88038ee442b232
+SIZE (phonopy-2.41.2.tar.gz) = 4713884