diff --git a/cpp/cmake_modules/UseCython.cmake b/cpp/cmake_modules/UseCython.cmake
index e15ac59490c..7d88daa4fad 100644
--- a/cpp/cmake_modules/UseCython.cmake
+++ b/cpp/cmake_modules/UseCython.cmake
@@ -184,4 +184,9 @@ function(cython_add_module _name pyx_target_name generated_files)
   add_dependencies(${_name} ${pyx_target_name})
 endfunction()
 
+execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from Cython.Compiler.Version import version; print(version)"
+                OUTPUT_VARIABLE CYTHON_VERSION_OUTPUT
+                OUTPUT_STRIP_TRAILING_WHITESPACE)
+set(CYTHON_VERSION "${CYTHON_VERSION_OUTPUT}")
+
 include(CMakeParseArguments)
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index a90dee70584..5d5eeaf8157 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -260,6 +260,7 @@ message(STATUS "Found NumPy version: ${Python3_NumPy_VERSION}")
 message(STATUS "NumPy include dir: ${NUMPY_INCLUDE_DIRS}")
 
 include(UseCython)
+message(STATUS "Found Cython version: ${CYTHON_VERSION}")
 
 # Arrow C++ and set default PyArrow build options
 include(GNUInstallDirs)
@@ -855,6 +856,10 @@ set(CYTHON_FLAGS "${CYTHON_FLAGS}" "--warning-errors")
 # undocumented Cython feature.
 set(CYTHON_FLAGS "${CYTHON_FLAGS}" "--no-c-in-traceback")
 
+if(CYTHON_VERSION VERSION_GREATER_EQUAL "3.1.0a0")
+  list(APPEND CYTHON_FLAGS "-Xfreethreading_compatible=True")
+endif()
+
 foreach(module ${CYTHON_EXTENSIONS})
   string(REPLACE "." ";" directories ${module})
   list(GET directories -1 module_name)