diff --git a/science/phonopy/Makefile b/science/phonopy/Makefile
index 5eb7e9e4183c..da19662d2ebc 100644
--- a/science/phonopy/Makefile
+++ b/science/phonopy/Makefile
@@ -1,26 +1,26 @@
 PORTNAME=	phonopy
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.48.0
+DISTVERSION=	3.0.1
 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 23f8a4ef34e1..0133368370bb 100644
--- a/science/phonopy/distinfo
+++ b/science/phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1771223031
-SHA256 (phonopy-phonopy-v2.48.0_GH0.tar.gz) = b1550e7ae23b271cb6cb4f403a9cb6ea9764e459273a23676a0a3353674c5014
-SIZE (phonopy-phonopy-v2.48.0_GH0.tar.gz) = 8083742
+TIMESTAMP = 1772765484
+SHA256 (phonopy-phonopy-v3.0.1_GH0.tar.gz) = d3888675d46d14ea64444aabb1593a7faab0b720b8d3fedc1fa4c137e1fc60a1
+SIZE (phonopy-phonopy-v3.0.1_GH0.tar.gz) = 8083779
diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile
index c5b0a759477c..4a12dcd223e1 100644
--- a/science/py-phonopy/Makefile
+++ b/science/py-phonopy/Makefile
@@ -1,39 +1,45 @@
 PORTNAME=	phonopy
-DISTVERSION=	2.48.0
+DISTVERSION=	3.0.1
 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} \
 		${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}
 
 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 2.41.2: 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)
+# 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
 
 .include <bsd.port.mk>
diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo
index 6f3136c2948f..8dd668c0733e 100644
--- a/science/py-phonopy/distinfo
+++ b/science/py-phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1771223090
-SHA256 (phonopy-2.48.0.tar.gz) = 206b5af9dba2dc557a1b5e14e7105d5f414700fcb0ba8e0a2029d1a40a557b43
-SIZE (phonopy-2.48.0.tar.gz) = 5077344
+TIMESTAMP = 1772765557
+SHA256 (phonopy-3.0.1.tar.gz) = ee60e6a9ef3b3aafc508609e797eea3ec558fe4a5e93c7cd259fd19248a0144d
+SIZE (phonopy-3.0.1.tar.gz) = 5077860
diff --git a/science/py-phonopy/files/patch-test_unfolding_plot__band.py b/science/py-phonopy/files/patch-test_unfolding_plot__band.py
new file mode 100644
index 000000000000..8cd07c453420
--- /dev/null
+++ b/science/py-phonopy/files/patch-test_unfolding_plot__band.py
@@ -0,0 +1,29 @@
+--- test/unfolding/plot_band.py.orig	2026-03-06 02:55:00 UTC
++++ test/unfolding/plot_band.py
+@@ -5,14 +5,16 @@ import sys
+ import matplotlib.pyplot as plt
+ import numpy as np
+ 
+-if len(sys.argv) > 1:
+-    filename = sys.argv[1]
+-else:
+-    filename = "bin-unfolding.dat"
++if __name__ == '__main__':
++    if len(sys.argv) > 1:
++        filename = sys.argv[1]
++    else:
++        filename = "bin-unfolding.dat"
+ 
+-x, y, z = np.loadtxt(filename).T
+-idx = z.argsort()
+-x, y, z = x[idx], y[idx], z[idx]
+-sc = plt.scatter(x, y, c=z, s=30, vmin=0, edgecolor=None, cmap="Greys")
+-plt.colorbar(sc)
+-plt.show()
++    x, y, z = np.loadtxt(filename).T
++    idx = z.argsort()
++    x, y, z = x[idx], y[idx], z[idx]
++    sc = plt.scatter(x, y, c=z, s=30, vmin=0, edgecolor=None, cmap="Greys")
++    plt.colorbar(sc)
++    plt.show()
++