How to fix ModuleNotFoundError: No module named 'Cython'

One error that you might encounter when working with Python is:

ModuleNotFoundError: No module named 'Cython'

This error occurs when Python can’t find the Cython module in your current Python environment.

This tutorial shows examples that cause this error and how to fix it.

How to reproduce the error

The Cython library is used to create C extensions for Python. You can compile your Python module into C for improved performance.

Suppose you import the cythonize function from the Cython.Build module in your code as follows:

from setuptools import setup
from Cython.Build import cythonize

    ext_modules = cythonize("extension.pyx")

But you get the following error when running the code:

Traceback (most recent call last):
  File "", line 2, in <module>
    from Cython.Build import cythonize
ModuleNotFoundError: No module named 'Cython'

This error occurs because the Cython module is not a built-in Python module, so you need to install it before using it.

How to fix this error

To resolve this error, you need to install the Cython package using pip as shown below:

pip install cython

# For pip3:
pip3 install cython

Once the module is installed, you should be able to run the code that imports Cython modules without receiving this error.

Install commands for other environments

The install command might differ depending on what environment you used to run the Python code.

Here’s a list of common install commands in popular Python environments:

# if you don't have pip in your PATH:
python -m pip install cython

python3 -m pip install cython

# Windows
py -m pip install cython

# Anaconda
conda install -c anaconda cython

# Jupyter Notebook
!pip install cython

Once the module is installed, you should be able to run the code without receiving this error.

Other common causes for this error

If you still see the error even after installing the package, it means that the Cython package can’t be found in your Python environment.

There are several reasons why this error can happen:

  1. You may have multiple versions of Python installed on your system, and you are using a different version of Python than the one where Cython is installed.
  2. You might have Cython installed in a virtual environment, and you are not activating the virtual environment before running your code.
  3. Your IDE uses a different version of Python from the one that has Cython

Let’s see how to fix these errors in practice.

Handling multiple versions of Python

If you have multiple versions of Python installed on your system, you need to make sure that you are using the specific version where the Cython module is available.

You can test this by running the which -a python or which -a python3 command from the terminal:

$ which -a python3

In the example above, there are two versions of Python installed on /opt/homebrew/bin/python3 and /usr/bin/python3.

Suppose you run the following steps in your project:

  1. Install Cython with pip using /usr/bin/ Python version
  2. Install Python using Homebrew, you have Python in /opt/homebrew/
  3. Then you run from Cython.Build import cythonize in your code

The steps above will cause the error because Cython is installed in /usr/bin/, and your code is probably executed using Python from /opt/homebrew/ path.

To solve this error, you need to run pip install Cython command again so that Cython is installed and accessible by the new Python version.

Next, you can also have Cython installed in a virtual environment.

Handling Python virtual environment

Python venv package allows you to create a virtual environment where you can install different versions of packages required by your project.

If you are installing Cython inside a virtual environment, then the module won’t be accessible outside of that environment.

You can see if a virtual environment is activated or not by looking at your command prompt.

When a virtual environment is activated, the name of that environment will be shown inside parentheses as shown below:

In the picture above, the name of the virtual environment (base) appears when the Conda virtual environment is activated.

You need to turn off the virtual environment so that pip installs to your computer.

When your virtual environment is created by Conda, run the conda deactivate command. Otherwise, running the deactivate command should work.

Handle IDE using a different Python version

Finally, the IDE from where you run your Python code may use a different Python version when you have multiple versions installed.

For example, you can check the Python interpreter used in VSCode by opening the command palette (CTRL + Shift + P for Windows and ⌘ + Shift + P for Mac) then run the Python: Select Interpreter command.

You should see all available Python versions listed as follows:

You need to use the same version where you installed Cython so that the module can be found when you run the code from VSCode.

Once done, you should be able to import Cython into your code.


In summary, the ModuleNotFoundError: No module named 'Cython' error occurs when the Cython package is not available in your Python environment. To fix this error, you need to install Cython using pip.

If you already have the module installed, make sure you are using the correct version of Python, deactivate the virtual environment if you have one, and check for the Python version used by your IDE.

By following these steps, you should be able to import cythonize function from the Cython.Build module in your code successfully.

I hope this tutorial is helpful. Happy coding! 👋

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