In Pycharm version 2017.3, you can go to
Pycharm -> Preferences -> Project -> Project Interpreter -> <project_name> -> settings button on the right of the python interpreter text box -> Add local
This will open a new window with virtualenv Environment as one of the options on the left. On Selecting it, you will get an option to make a new virtualenv environment or use an existing virtual environment. Here next to the dropdown text box, you can click “…” and browse to your existing virtualenv created using pyenv and select it. It will select this virtualenv when you start terminal from Pycharm and also use the corresponding python interpreter as set while creating that virtualenv.
