The versatile 22 year-old, who can play in the back row or second row, made his debut for Ulster, against Connacht, in April 2012 and he has made 41 appearances for the province so far.
His excellent form for Ulster at the start of the 2012/13 season saw him fast-tracked into the Ireland squad and he won his first international cap in November 2012, against South Africa.
He has now played 14 times for Ireland, most recently as a second half replacement in the win over France last weekend.
He lined-out in four of Ireland's five matches in the 2014 RBS 6 Nations Championship win and started both games in Ireland's tour of Argentina last summer.
Iain is a former pupil of Belfast Royal Academy and progressed through the Hughes Insurance Ulster Academy before signing his first senior contract in October 2012.
As well as his senior international appearances, he has also represented Ireland at U19, U20 and has played three times for the Wolfhounds, including the match against England Saxons at Irish Independent Park last month.
His new contract means that he will be at Kingspan Stadium until at least the summer of 2018.
Commenting on his new contract, Henderson said: "I am delighted to have signed for another three seasons and I am aiming to be an integral part of the team going forward.
"As a proud Ulsterman it remains a massive honour to play for Ulster Rugby. By signing a new contract, it allows me to focus on achieving my personal goals alongside the ambitions here at Kingspan Stadium. I am very much looking forward to the next three years."
Ulster Rugby's Team Manager, Bryn Cunningham added: "Iain is without doubt one of the most exciting young players in European Rugby. An exceptionally powerful runner with ball-in-hand, his strength and high work-rate around the park make him a vital member of our squad.
"As we seek to build a team around a core group of highly talented, homegrown Ulster players, retaining the services of someone like Iain was hugely important to us.
"We know that with his ability and with what he has achieved already in the game that there were other leading European clubs extremely keen to sign him, therefore I am delighted that he has committed to his home province for a further three seasons."
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