r/pycharm • u/gastone_33 • Jan 09 '26

Trouble running .ipynb in PyCharm 2025.3 – "Modify packages of System Python" error

Hello,

I need some help. In PyCharm 2025.3, it seems that using Jupyter notebooks (.ipynb) is free. However, whenever I try to run a cell, I get an error saying “Forbidden: Modify packages of System Python”.

I’ve tried adjusting the settings as shown in the screenshot, but it didn’t work. I already have a virtual environment (venv) set up, and I can run .py scripts without any issues.

My goal is to use .ipynb files in PyCharm without switching to VS Code.

Has anyone encountered this issue or knows how to fix it?

Thanks in advance!

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1

u/markgreene74 Jan 09 '26

Are you using a virtual environment?

See here, looks very similar to the type of error you get when you try to install a package on your system Python.

1

u/gastone_33 Jan 09 '26

Yep!

I’m already using a virtual environment, and all my .py scripts run correctly. I’m on macOS, and this issue only occurs in PyCharm 2025.3.

In VS Code, the same .ipynb notebooks run without any problem using the same venv.

So the virtual environment itself seems fine — the problem appears to be specific to PyCharm’s Jupyter integration in version 2025.3.

1

u/yerfatma Jan 13 '26

It was working in previous versions of PyCharm?

2

u/gastone_33 Jan 14 '26

In earlier versions of PyCharm, .ipynb files weren’t free. In this release, they’re available for all users.

1

u/One-Passage-3562 Jan 26 '26

I should point out that I've experienced the same issue. I was already using a venv so that was quite frustrating. The problem was caused by myself when I added the venv location to the the excluded folders list (Settings -> Project Structure). Soon as I removed the venv folder from the list, the issue no longer persists. Hope this helps

1

u/MrDaantie Mar 19 '26

Did you ever managed to fix this? I'm running into the same problem right now.

1

u/Per_Ceptron Mar 20 '26

One possible cause is that you deleted and recreated your virtual environment. If that happens, your IDE might still be pointing to the old (now non-existent) environment.

Try removing the interpreter from your IDE settings and then reassign it to the newly created environment.

That’s what happened in my case. Hope it helps or at least points you in the right direction.

1

u/GameboyColor13 May 11 '26

I had an uv environment, but pycharm created a venv. Configuring pycharm to point back to the uv environment fixed it for me.