diff --git a/science/py-scikit-learn/Makefile b/science/py-scikit-learn/Makefile
index c453d64cde45..e5bd78a3f25a 100644
--- a/science/py-scikit-learn/Makefile
+++ b/science/py-scikit-learn/Makefile
@@ -1,38 +1,37 @@
 PORTNAME=	scikit-learn
-DISTVERSION=	1.8.0
-PORTREVISION=	2
+DISTVERSION=	1.9.0
 CATEGORIES=	science python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 DISTNAME=	scikit_learn-${DISTVERSION}
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Machine learning algorithms for python
 WWW=		https://scikit-learn.org/
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/COPYING
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}joblib>=1.3.0:devel/py-joblib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.10.0:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}threadpoolctl>=3.2.0:devel/py-threadpoolctl@${PY_FLAVOR}
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 BUILD_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}meson-python>=0.17.1:devel/meson-python@${PY_FLAVOR}
 
 USES=		fortran python localbase shebangfix
 USE_PYTHON=	autoplist cython pep517 pytest
 
 TEST_ARGS=	sklearn
 TEST_WRKSRC=	${STAGEDIR}${PYTHON_SITELIBDIR}
 
 SHEBANG_FILES=	sklearn/_build_utils/version.py
 BINARY_ALIAS=	cython=cython-${PYTHON_VER}
 
 post-install: # strip binaries
 	@${STRIP_CMD} \
 		${STAGEDIR}${PYTHON_SITELIBDIR}/sklearn/*.cpython*.so \
 		${STAGEDIR}${PYTHON_SITELIBDIR}/sklearn/*/*.cpython*.so \
 		${STAGEDIR}${PYTHON_SITELIBDIR}/sklearn/*/*/*.cpython*.so
 
 .include <bsd.port.mk>
diff --git a/science/py-scikit-learn/distinfo b/science/py-scikit-learn/distinfo
index 43958a1e6660..baefb6bf489d 100644
--- a/science/py-scikit-learn/distinfo
+++ b/science/py-scikit-learn/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1772326808
-SHA256 (scikit_learn-1.8.0.tar.gz) = 9bccbb3b40e3de10351f8f5068e105d0f4083b1a65fa07b6634fbc401a6287fd
-SIZE (scikit_learn-1.8.0.tar.gz) = 7335585
+TIMESTAMP = 1780505264
+SHA256 (scikit_learn-1.9.0.tar.gz) = 8833266989d3a5110178a9fae30783675460724d0e1efb13b14901d2c660c557
+SIZE (scikit_learn-1.9.0.tar.gz) = 7750767
diff --git a/science/py-scikit-learn/files/patch-pyproject.toml b/science/py-scikit-learn/files/patch-pyproject.toml
index 6afd5e2f3c98..a0335ac85dae 100644
--- a/science/py-scikit-learn/files/patch-pyproject.toml
+++ b/science/py-scikit-learn/files/patch-pyproject.toml
@@ -1,23 +1,12 @@
---- pyproject.toml.orig	2025-12-09 16:13:35 UTC
+--- pyproject.toml.orig	2026-06-02 08:32:39 UTC
 +++ pyproject.toml
-@@ -13,8 +13,7 @@ requires-python = ">=3.11"
-   "threadpoolctl>=3.2.0",
+@@ -14,8 +14,7 @@ requires-python = ">=3.11"
+   "threadpoolctl>=3.5.0",
  ]
  requires-python = ">=3.11"
 -license = "BSD-3-Clause"
 -license-files = ["COPYING"]
 +license = {text="BSD-3-Clause"}
  classifiers=[
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
-@@ -97,8 +96,8 @@ requires = [
- requires = [
-     "meson-python>=0.17.1,<0.19.0",
-     "cython>=3.1.2,<3.3.0",
--    "numpy>=2,<2.4.0",
--    "scipy>=1.10.0,<1.17.0",
-+    "numpy",
-+    "scipy>=1.10.0",
- ]
- 
- [tool.pytest.ini_options]