diff --git a/manifest/armv7l/p/py3_cython.filelist b/manifest/armv7l/p/py3_cython.filelist
index 8201067d2..87811ad66 100644
--- a/manifest/armv7l/p/py3_cython.filelist
+++ b/manifest/armv7l/p/py3_cython.filelist
@@ -397,7 +397,6 @@
 /usr/local/lib/python3.13/site-packages/Cython/Utility/ExtensionTypes.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/FunctionArguments.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/ImportExport.c
-/usr/local/lib/python3.13/site-packages/Cython/Utility/Lock.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/MemoryView.pxd
 /usr/local/lib/python3.13/site-packages/Cython/Utility/MemoryView.pyx
 /usr/local/lib/python3.13/site-packages/Cython/Utility/MemoryView_C.c
@@ -409,6 +408,7 @@
 /usr/local/lib/python3.13/site-packages/Cython/Utility/Printing.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/Profile.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/StringTools.c
+/usr/local/lib/python3.13/site-packages/Cython/Utility/Synchronization.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/TestCyUtilityLoader.pyx
 /usr/local/lib/python3.13/site-packages/Cython/Utility/TestCythonScope.pyx
 /usr/local/lib/python3.13/site-packages/Cython/Utility/TestUtilityLoader.c
@@ -432,15 +432,15 @@
 /usr/local/lib/python3.13/site-packages/Cython/__pycache__/__init__.cpython-313.pyc
 /usr/local/lib/python3.13/site-packages/Cython/py.typed
 /usr/local/lib/python3.13/site-packages/__pycache__/cython.cpython-313.pyc
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/COPYING.txt
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/INSTALLER
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/LICENSE.txt
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/METADATA
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/RECORD
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/REQUESTED
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/WHEEL
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/entry_points.txt
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/top_level.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/COPYING.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/INSTALLER
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/LICENSE.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/METADATA
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/RECORD
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/REQUESTED
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/WHEEL
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/entry_points.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/top_level.txt
 /usr/local/lib/python3.13/site-packages/cython.py
 /usr/local/lib/python3.13/site-packages/pyximport/__init__.py
 /usr/local/lib/python3.13/site-packages/pyximport/__pycache__/__init__.cpython-313.pyc
diff --git a/manifest/i686/p/py3_cython.filelist b/manifest/i686/p/py3_cython.filelist
index 1ea3f4dce..15793f630 100644
--- a/manifest/i686/p/py3_cython.filelist
+++ b/manifest/i686/p/py3_cython.filelist
@@ -412,7 +412,6 @@
 /usr/local/lib/python3.13/site-packages/Cython/Utility/ExtensionTypes.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/FunctionArguments.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/ImportExport.c
-/usr/local/lib/python3.13/site-packages/Cython/Utility/Lock.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/MemoryView.pxd
 /usr/local/lib/python3.13/site-packages/Cython/Utility/MemoryView.pyx
 /usr/local/lib/python3.13/site-packages/Cython/Utility/MemoryView_C.c
@@ -424,6 +423,7 @@
 /usr/local/lib/python3.13/site-packages/Cython/Utility/Printing.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/Profile.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/StringTools.c
+/usr/local/lib/python3.13/site-packages/Cython/Utility/Synchronization.c
 /usr/local/lib/python3.13/site-packages/Cython/Utility/TestCyUtilityLoader.pyx
 /usr/local/lib/python3.13/site-packages/Cython/Utility/TestCythonScope.pyx
 /usr/local/lib/python3.13/site-packages/Cython/Utility/TestUtilityLoader.c
@@ -448,15 +448,15 @@
 /usr/local/lib/python3.13/site-packages/Cython/__pycache__/__init__.cpython-313.pyc
 /usr/local/lib/python3.13/site-packages/Cython/py.typed
 /usr/local/lib/python3.13/site-packages/__pycache__/cython.cpython-313.pyc
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/INSTALLER
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/METADATA
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/RECORD
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/REQUESTED
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/WHEEL
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/entry_points.txt
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/licenses/COPYING.txt
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/licenses/LICENSE.txt
-/usr/local/lib/python3.13/site-packages/cython-3.1.2.dist-info/top_level.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/INSTALLER
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/METADATA
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/RECORD
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/REQUESTED
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/WHEEL
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/entry_points.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/licenses/COPYING.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/licenses/LICENSE.txt
+/usr/local/lib/python3.13/site-packages/cython-3.1.3.dist-info/top_level.txt
 /usr/local/lib/python3.13/site-packages/cython.py
 /usr/local/lib/python3.13/site-packages/pyximport/__init__.py
 /usr/local/lib/python3.13/site-packages/pyximport/__pycache__/__init__.cpython-313.pyc
diff --git a/manifest/x86_64/p/py3_cython.filelist b/manifest/x86_64/p/py3_cython.filelist
index 80a8b5b42..f24d3d7a0 100644
--- a/manifest/x86_64/p/py3_cython.filelist
+++ b/manifest/x86_64/p/py3_cython.filelist
@@ -412,7 +412,6 @@
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/ExtensionTypes.c
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/FunctionArguments.c
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/ImportExport.c
-/usr/local/lib64/python3.13/site-packages/Cython/Utility/Lock.c
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/MemoryView.pxd
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/MemoryView.pyx
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/MemoryView_C.c
@@ -424,6 +423,7 @@
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/Printing.c
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/Profile.c
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/StringTools.c
+/usr/local/lib64/python3.13/site-packages/Cython/Utility/Synchronization.c
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/TestCyUtilityLoader.pyx
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/TestCythonScope.pyx
 /usr/local/lib64/python3.13/site-packages/Cython/Utility/TestUtilityLoader.c
@@ -448,15 +448,15 @@
 /usr/local/lib64/python3.13/site-packages/Cython/__pycache__/__init__.cpython-313.pyc
 /usr/local/lib64/python3.13/site-packages/Cython/py.typed
 /usr/local/lib64/python3.13/site-packages/__pycache__/cython.cpython-313.pyc
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/INSTALLER
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/METADATA
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/RECORD
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/REQUESTED
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/WHEEL
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/entry_points.txt
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/licenses/COPYING.txt
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/licenses/LICENSE.txt
-/usr/local/lib64/python3.13/site-packages/cython-3.1.2.dist-info/top_level.txt
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/INSTALLER
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/METADATA
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/RECORD
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/REQUESTED
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/WHEEL
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/entry_points.txt
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/licenses/COPYING.txt
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/licenses/LICENSE.txt
+/usr/local/lib64/python3.13/site-packages/cython-3.1.3.dist-info/top_level.txt
 /usr/local/lib64/python3.13/site-packages/cython.py
 /usr/local/lib64/python3.13/site-packages/pyximport/__init__.py
 /usr/local/lib64/python3.13/site-packages/pyximport/__pycache__/__init__.cpython-313.pyc
diff --git a/packages/py3_cython.rb b/packages/py3_cython.rb
index 424155c26..7c5807281 100644
--- a/packages/py3_cython.rb
+++ b/packages/py3_cython.rb
@@ -3,17 +3,17 @@ require 'buildsystems/pip'
 class Py3_cython < Pip
   description 'The Cython language makes writing C extensions for the Python language as easy as Python itself.'
   homepage 'https://cython.org/'
-  version "3.1.2-#{CREW_PY_VER}"
+  version "3.1.3-#{CREW_PY_VER}"
   license 'Apache-2.0'
   compatibility 'all'
   source_url 'SKIP'
   binary_compression 'tar.zst'
 
   binary_sha256({
-    aarch64: '22e60b598705ae694e5869e59f0bf3f114cada507ff825ee06ccb3c83122971c',
-     armv7l: '22e60b598705ae694e5869e59f0bf3f114cada507ff825ee06ccb3c83122971c',
-       i686: '1506fdf6e57c617390606290aa88e3126d794da93c4c623a0d81f9cb42b406ad',
-     x86_64: '5bb5a4740edf30e890ac0097a7d32012b63480c25d1d5a509d3e42fdee499822'
+    aarch64: '9f3674d0ccbc5b55e35a8650ea0e7aff5a56b98b8d290998dbf2bb4cd4261993',
+     armv7l: '9f3674d0ccbc5b55e35a8650ea0e7aff5a56b98b8d290998dbf2bb4cd4261993',
+       i686: '2bd6e9c3a124a4b7aadcc72de5e9305429edfca725b92b9dd354e3e2fefa322d',
+     x86_64: '62559a10f612a428cb91104d46515a66e4cf657ba98d850d09735005303f91fd'
   })
 
   depends_on 'glibc' # R