diff --git a/asv_bench/asv.conf.json b/asv_bench/asv.conf.json
index 30c692115eab1..d286e57ce6b51 100644
--- a/asv_bench/asv.conf.json
+++ b/asv_bench/asv.conf.json
@@ -42,7 +42,7 @@
     // followed by the pip installed packages).
     "matrix": {
         "pip+build": [],
-        "Cython": ["3.0"],
+        "Cython": [],
         "matplotlib": [],
         "sqlalchemy": [],
         "scipy": [],
diff --git a/ci/deps/actions-310-minimum_versions.yaml b/ci/deps/actions-310-minimum_versions.yaml
index f8522594f36f4..eaba29c2f796e 100644
--- a/ci/deps/actions-310-minimum_versions.yaml
+++ b/ci/deps/actions-310-minimum_versions.yaml
@@ -8,7 +8,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/ci/deps/actions-310.yaml b/ci/deps/actions-310.yaml
index ea22bc411dedd..fbeabb56a62d0 100644
--- a/ci/deps/actions-310.yaml
+++ b/ci/deps/actions-310.yaml
@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/ci/deps/actions-311-downstream_compat.yaml b/ci/deps/actions-311-downstream_compat.yaml
index e981be9891dec..07f865868573d 100644
--- a/ci/deps/actions-311-downstream_compat.yaml
+++ b/ci/deps/actions-311-downstream_compat.yaml
@@ -7,7 +7,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/ci/deps/actions-311-numpydev.yaml b/ci/deps/actions-311-numpydev.yaml
index 325a6d45d74fd..99cbe0415b4f9 100644
--- a/ci/deps/actions-311-numpydev.yaml
+++ b/ci/deps/actions-311-numpydev.yaml
@@ -8,7 +8,7 @@ dependencies:
   - versioneer
   - meson=1.2.1
   - meson-python=0.13.1
-  - cython>=0.29.33
+  - cython<4.0.0a0
 
   # test dependencies
   - pytest>=7.3.2
diff --git a/ci/deps/actions-311-pyarrownightly.yaml b/ci/deps/actions-311-pyarrownightly.yaml
index 2d3d11c294e12..da0cecda0fb46 100644
--- a/ci/deps/actions-311-pyarrownightly.yaml
+++ b/ci/deps/actions-311-pyarrownightly.yaml
@@ -7,7 +7,7 @@ dependencies:
   # build dependencies
   - versioneer
   - meson=1.2.1
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson-python=0.13.1
 
   # test dependencies
diff --git a/ci/deps/actions-311.yaml b/ci/deps/actions-311.yaml
index f03d518fd22fb..9ab82d69504fb 100644
--- a/ci/deps/actions-311.yaml
+++ b/ci/deps/actions-311.yaml
@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/ci/deps/actions-312.yaml b/ci/deps/actions-312.yaml
index 58c6c2ca3210c..d12fe4f7d6e49 100644
--- a/ci/deps/actions-312.yaml
+++ b/ci/deps/actions-312.yaml
@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/ci/deps/actions-313-freethreading.yaml b/ci/deps/actions-313-freethreading.yaml
index d10c70bc1fbfb..14e3ade976b01 100644
--- a/ci/deps/actions-313-freethreading.yaml
+++ b/ci/deps/actions-313-freethreading.yaml
@@ -7,6 +7,7 @@ dependencies:
   # build dependencies
   - setuptools
   - versioneer
+  - cython<4.0.0a0
   - meson=1.8.0
   - meson-python=0.18.0
 
@@ -21,10 +22,8 @@ dependencies:
   # optional dependencies
   - hypothesis>=6.84.0
 
-  # Move Cython to build dependencies, once they release a version that supports freethreading
   - pip:
     # No free-threaded coveragepy (with the C-extension) on conda-forge yet
     - pytest-cov
     - "tzdata>=2022.7"
     - "--extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
-    - "cython"
diff --git a/ci/deps/actions-313.yaml b/ci/deps/actions-313.yaml
index f94138a98e127..57ed0ea062398 100644
--- a/ci/deps/actions-313.yaml
+++ b/ci/deps/actions-313.yaml
@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/ci/deps/actions-pypy-39.yaml b/ci/deps/actions-pypy-39.yaml
index 90933b24b88db..e0ddc6954e4a4 100644
--- a/ci/deps/actions-pypy-39.yaml
+++ b/ci/deps/actions-pypy-39.yaml
@@ -9,7 +9,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython>=0.29.33
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/environment.yml b/environment.yml
index 6300e32b5a1b5..8926c85143e2b 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,7 +8,7 @@ dependencies:
 
   # build dependencies
   - versioneer
-  - cython~=3.0.5
+  - cython<4.0.0a0
   - meson=1.2.1
   - meson-python=0.13.1
 
diff --git a/pyproject.toml b/pyproject.toml
index 370bd0e0605cb..b17a1eacfa717 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ requires = [
     "meson-python>=0.13.1",
     "meson>=1.2.1,<2",
     "wheel",
-    "Cython==3.1.0rc1",  # Note: sync with setup.py, environment.yml and asv.conf.json
+    "Cython<4.0.0a0",  # Note: sync with setup.py, environment.yml and asv.conf.json
     # Force numpy higher than 2.0rc1, so that built wheels are compatible
     # with both numpy 1 and 2
     "numpy>=2.0.0rc1",
diff --git a/requirements-dev.txt b/requirements-dev.txt
index c2bac550bc664..6515797bc3b9d 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -3,7 +3,7 @@
 
 pip
 versioneer[toml]
-cython~=3.0.5
+cython<4.0.0a0
 meson[ninja]==1.2.1
 meson-python==0.13.1
 pytest>=7.3.2