Why does PyCharm give unresolved reference errors on some Numpy imports?

The reason you are getting this is because of PyCharm's static analysis. Now, what Python does is use static skeletons (some are pre-generated and some are generated) to give you the analysis. Take a look at the pre-generated skeletons here -> https://github.com/JetBrains/python-skeletons

This might be solved, by enabling the following:

However, if that does not work:

which will block off the error, it will appear as a comment above the line.

The Python configuration is specified in (at least) two places: Run | Edit Configurations | Python | Python Interpreter, and File | Settings | Project | Project Interpreter. My mistake was I did not set the correct Python installation in the File | Settings .... Hence, it was referring to a Python configuration that did not have the import installed (e.g. NumPy).

After I set these two locations to point to the same, correct Python installation, I did a File | Invalidate Caches / Restart, then it was fine.

A third place to check is File | Default Settings... | Project Interpreter and make sure it matches the other settings.