A former pupil of Belfast Royal Academy, the 20-year-old has represented Ulster and Ireland at numerous underage levels and has progressed through the Ulster Academy system.
He played for the Ireland Under-20s in the previous two IRB Junior World Championships and was one of the standout players in this summer's tournament in South Africa.
The contract has capped a fantastic few months for the youngster. He made his senior debut for Ulster as a replacement in the RaboDirect PRO12 loss to Connacht last April.
The following month Henderson marked his first start with a fine individual try against Munster at Thomond Park, a score which came courtesy of an explosive run down the touchline.
Commenting on the announcement, Henderson said: "I'm delighted to have signed a new contract with Ulster. I've dreamed of being a professional with my home province and it's fantastic that it has come to fruition.
"I've learnt a great deal from the coaching staff and senior players here and I can't wait to continue my development at Ravenhill. There's a lot of competition in the squad, particularly in the back row, but I want to try and get as many games as possible under my belt."
Ulster director of rugby David Humphreys added: "Iain is one of the brightest young players in Ireland, he has all the attributes required to be a top class forward and we are delighted to welcome him into the professional set-up.
"We are trying to build a team of homegrown players which is capable of competing with and beating the best teams in Europe, and Iain epitomises what we are trying to achieve.
"His performance against Cardiff a couple of weeks ago underlined his massive potential, but also showed that he is able to play at this level now. The exciting thing for us is that he will only get better."