The fresh terms keep the 23-year-old at Goodison Park until the end of June 2021.
Bosnia-Herzegovina international Besic joined Everton from Hungarian side Ferencvaros in July 2014 and has made 40 first-team appearances to date.
"I'm really happy to have signed a new contract with a club such as Everton," Besic told Everton TV.
"After a year-and-a-half with the club, it makes me proud that they have given me a new deal.
"When I first arrived here it was difficult for me, but now I feel at home. The supporters, as well as the manager, the staff and my team-mates, have all made me welcome at the club and I feel really happy.
"It was very easy when I heard about it. It was clear that I wanted to stay and sign the new contract.
"When people look at my game, before and now, I think I have improved a lot in many different areas. But, like you have seen, I am still adapting to the league and I will continue to work hard and give my best.
"We always speak about things we want to achieve, Europe and other things. We have to show it on the pitch and do it. The next 12 games and also Chelsea in the FA Cup, I hope we can do our speaking on the pitch."