PyCharm Jupyter Notebook SQL Cell Integration Malfunction
Issue Summary
When using Jupyter Notebook inside PyCharm, SQL cells do not show the Data Source Selector. SQL statements executed within SQL cells fail, although the same statements run correctly in a standard Python code cell using the %%sql magic command.
Additionally, after restarting PyCharm, code cells that originally used the %%sql magic are automatically converted into SQL cells, but they also fail to run properly.
Details
- Creating an SQL cell in PyCharm’s Jupyter Notebook does not show the Data Source dropdown selector.
- Executing SQL queries directly in SQL cells results in errors.
- The same SQL queries run correctly when using
%%sqlin a regular Python code cell. - After restarting PyCharm, code cells that previously used
%%sqlare automatically transformed into SQL cells, and these converted SQL cells also fail to run.

This suggests that PyCharm’s SQL cell integration is not correctly recognizing, loading, or binding the configured data source, whereas the IPython %%sql magic behaves normally.
Please advise whether this is a known issue, a configuration problem, or a bug in the SQL/Jupyter integration. Thank you!
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Hi Zyl020918
This is is unfortunately a known bug introduced in PyCharm 2025.2.3 (YT link )
Normally, when you create an SQL cell, in the top of the cell you get an extra tab where you can configure the data source.
https://www.jetbrains.com/help/pycharm/2025.2/working-with-sql-cells.html#-2x2fp9_6
This is currently broken in the latest PyCharm 2025.2.4 however it is fixed in PyCharm latest EAP 2025.3 EAP which you can download from here
Alternatively, in case you would like to wait for the stable release, in early December is planned the release of 2025.3.0
Please let me know if any further questions,
Kind regards,