diff --git a/ci/docker/python-wheel-manylinux.dockerfile b/ci/docker/python-wheel-manylinux.dockerfile
index d22a70a2d77..452809ad09c 100644
--- a/ci/docker/python-wheel-manylinux.dockerfile
+++ b/ci/docker/python-wheel-manylinux.dockerfile
@@ -114,5 +114,10 @@ RUN PYTHON_ROOT=$(find /opt/python -name cp${PYTHON_VERSION/./}-${PYTHON_ABI_TAG
 SHELL ["/bin/bash", "-i", "-c"]
 ENTRYPOINT ["/bin/bash", "-i", "-c"]
 
+# Remove once there are released Cython wheels for 3.13 free-threaded available
+RUN if [ "${python_abi_tag}" = "cp313t" ]; then \
+      pip install cython --pre --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" --prefer-binary ; \
+    fi
+
 COPY python/requirements-wheel-build.txt /arrow/python/
 RUN pip install -r /arrow/python/requirements-wheel-build.txt
diff --git a/ci/scripts/python_wheel_macos_build.sh b/ci/scripts/python_wheel_macos_build.sh
index d2c392e6b9d..91925e7abe8 100755
--- a/ci/scripts/python_wheel_macos_build.sh
+++ b/ci/scripts/python_wheel_macos_build.sh
@@ -49,8 +49,15 @@ fi
 echo "=== (${PYTHON_VERSION}) Install Python build dependencies ==="
 export PIP_SITE_PACKAGES=$(python -c 'import site; print(site.getsitepackages()[0])')
 
+# Remove once there are released Cython wheels for 3.13 free-threaded available
+FREE_THREADED_BUILD="$(python -c"import sysconfig; print(bool(sysconfig.get_config_var('Py_GIL_DISABLED')))")"
+if [[ $FREE_THREADED_BUILD == "True"  ]]; then
+  pip install cython --pre --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" --prefer-binary
+fi
+# With Python 3.9, the `--upgrade` flag is required to force full replacement of setuptools' distutils patching
+pip install --upgrade --target $PIP_SITE_PACKAGES "setuptools>=58"
+
 pip install \
-  --upgrade \
   --only-binary=:all: \
   --target $PIP_SITE_PACKAGES \
   -r ${source_dir}/python/requirements-wheel-build.txt
diff --git a/python/requirements-wheel-build.txt b/python/requirements-wheel-build.txt
index 2d448004768..faa078d3d7f 100644
--- a/python/requirements-wheel-build.txt
+++ b/python/requirements-wheel-build.txt
@@ -1,8 +1,3 @@
-# Remove pre and extra index url once there's NumPy and Cython wheels for 3.13
-# on PyPI
---pre
---extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
-
 cython>=0.29.31
 oldest-supported-numpy>=0.14; python_version<'3.9'
 numpy>=2.0.0; python_version>='3.9'
diff --git a/python/requirements-wheel-test.txt b/python/requirements-wheel-test.txt
index d129ac753ab..c051efb0aaa 100644
--- a/python/requirements-wheel-test.txt
+++ b/python/requirements-wheel-test.txt
@@ -1,9 +1,3 @@
-# Remove pre and extra index url once there's NumPy and Cython wheels for 3.13
-# on PyPI
---pre
---prefer-binary
---extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
-
 cffi
 cython
 hypothesis