diff --git a/science/phonopy/Makefile b/science/phonopy/Makefile
index be8c4ead95fd..dfe8e60a441f 100644
--- a/science/phonopy/Makefile
+++ b/science/phonopy/Makefile
@@ -1,26 +1,26 @@
 PORTNAME=	phonopy
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.4.0
+DISTVERSION=	3.5.1
 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 7a6c5a2b9ab1..c349b0fdb493 100644
--- a/science/phonopy/distinfo
+++ b/science/phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1774757814
-SHA256 (phonopy-phonopy-v3.4.0_GH0.tar.gz) = 021c8b4100540dbd3cb0fb4cef9e060a2339ab0c92b7033259de1cad9e42ae1d
-SIZE (phonopy-phonopy-v3.4.0_GH0.tar.gz) = 8136328
+TIMESTAMP = 1777008346
+SHA256 (phonopy-phonopy-v3.5.1_GH0.tar.gz) = 2aeaf0e363054c61e12b4948207cec5ddd70a50b68c9520fe813fe1e65439e2a
+SIZE (phonopy-phonopy-v3.5.1_GH0.tar.gz) = 8136506
diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile
index 566821844f21..d680aff30ef0 100644
--- a/science/py-phonopy/Makefile
+++ b/science/py-phonopy/Makefile
@@ -1,53 +1,42 @@
 PORTNAME=	phonopy
-DISTVERSION=	3.4.0
-PORTREVISION=	1
+DISTVERSION=	3.5.1
 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} \
 		${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \
 		${PY_SETUPTOOLS} \
 		${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}h5py>=3.0:science/py-h5py@${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}
 
 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 3.0.1: (see https://github.com/phonopy/phonopy/issues/739)
-# Results (47.21s):
-#         26 failed
-#        183 passed
-#          6 skipped
-#         53 warnings
-#        272 errors
-
-# tests as of 3.4.0:
-# Results (59.91s):
-#        380 failed
-#       1997 passed
-#         22 skipped
-#         52 warnings
+# tests as of 3.5.1:
+# Results (64.10s (0:01:04)):
+#      880 passed
+#       22 skipped
 
 .include <bsd.port.mk>
diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo
index df4fa0631068..45a200b76146 100644
--- a/science/py-phonopy/distinfo
+++ b/science/py-phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1774759850
-SHA256 (phonopy-3.4.0.tar.gz) = a4adc0ad23758c2b2459cd2ecf3c37a91a70fc7276bf83d79a853d36a80a15e3
-SIZE (phonopy-3.4.0.tar.gz) = 5127145
+TIMESTAMP = 1777015315
+SHA256 (phonopy-3.5.1.tar.gz) = 37869c383d0b1fa1355f17a1bb3599479406530d730791d71dc16186848db196
+SIZE (phonopy-3.5.1.tar.gz) = 5128062
diff --git a/science/py-phonopy/files/patch-test_conftest.py b/science/py-phonopy/files/patch-test_conftest.py
new file mode 100644
index 000000000000..af2e20741878
--- /dev/null
+++ b/science/py-phonopy/files/patch-test_conftest.py
@@ -0,0 +1,23 @@
+-- Fix test crash by setting matplotlib to use non-interactive Agg backend.
+-- This prevents segmentation faults when matplotlib tries to use GTK4 backend
+-- in a headless FreeBSD environment during test execution.
+-- See: https://github.com/phonopy/phonopy/issues/???
+
+--- test/conftest.py.orig	2026-04-24 07:29:40 UTC
++++ test/conftest.py
+@@ -5,12 +5,15 @@ from collections.abc import Callable
+ import pathlib
+ from collections.abc import Callable
+ 
++import matplotlib
+ import numpy as np
+ import pytest
+ 
+ import phonopy
+ from phonopy import Phonopy
+ from phonopy.structure.atoms import PhonopyAtoms
++
++matplotlib.use("Agg")
+ 
+ cwd = pathlib.Path(__file__).parent
+