Wilson, 30, was Ulster's player of the season in 2007 and he moved to Northampton the following year, where he has made over 100 appearances and helped the Saints win the European Challenge Cup and the LV= Cup.
Northampton have been linked with the Gloucester captain Luke Narraway as a potential replacement for Wilson.
Wilson said: "I've really enjoyed my time at Northampton and the club have been very good to me.
"Dorian West is an excellent forwards coach, Jim Mallinder's knowledge of the game is outstanding and I'd like to think that I've learnt a lot from them over the last four years and I can add that experience to Ulster.
"Northampton are a quality team and have an excellent set-up at the club but I suppose it was always in the back of my mind that I would like to finish my career at Ulster.
"I was born and raised there, learnt my rugby there and at the end of the day it is home. I'm delighted to be coming back."
Wilson is a potential replacement for Ulster's South African number eight Pedrie Wannenburg, who signed in 2010 on a two-year contract.
"While the back row is already a competitive area, the addition of Roger to the squad will provide us with the depth we need to ensure we are competitive in both the RaboDirect PRO12 and the Heineken Cup," Ulster's director of rugby David Humphreys said.
"He's currently playing the best rugby of his career and we're delighted that he has decided to return to Ulster next season and to commit his long-term future to the club."
Ulster are sixth in the PRO12 and top of their Heineken Cup group after last weekend's stunning 41-7 victory over Leicester at Ravenhill.
"The last couple of seasons have shown that Ulster are a club that can compete and compete to win things. They're now considered one of the top European teams and that they're genuine contenders for silverware," Wilson said.
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