As far as I know, Google App Engine supports https endpoints when using a regular environment:
https://cloud.google.com/appengine/docs/python/config/appref#handlers_secure
Yet, I couldn't figure out how to configure the app.yaml file to support https with a flexible environment. Any pointers?
From the documentation it looks like you do not have to do anything special in app.yaml to configure https for your application with appspot.com address.
In case you are looking to use Custom domains for your application (instead of appspot.com), then take a look at this page to configure SSL certificate for your custom domain.