I think I found the answer. I was having the same problem. In PyCharm Professional 2017.3, go to File | Settings | Tools | Python Scientific. There is an option there to “Show plots in toolwindow”. Uncheck this option. Then it should work ok. It has something to do with PyCharm trying to help you by allowing you to interact with your plots – as hinted at in this issue discussion. https://youtrack.jetbrains.com/issue/PY-26652