When the Deadpool movie is released in February of 2016, it will be taking place in the same cinematic universe as the rest of the X-Men franchise.
In a conversation with comicbook.com, X-Men: Days of Future Past writer Simon Kinberg had the following to say about the timelines of all these X-Men (and X-Men-related) movies:
“I guess I would say it's part of certainly an overall timeline and thought process that goes into these films, some of which is inspired by the comics and some which is inspired by seeing what Marvel's done with telling a larger tapestry and linking all those movies together, even as they stand independently as well. The same kind of thought is going to go into these X-Men movies at Fox.”
Given the proximity between Deadpool and the release of X-Men: Apocalypse just a few months later, it would seem likely that the films will be strongly connected in some way. Just how that comes to fruition remains to be seen.
[via Comic Book Resources]