The back rower made 29 appearances for Ulster last season, more than any other player with the exception of Pedrie Wannenburg, who also appeared in 29 games.
Henry's role as a key member of the team which reached the league play-offs and the Heineken Cup quarter-finals was recognised with a nomination for the Player of the Year honour at the Ulster Rugby Awards last May.
This season Henry was handed the captaincy by head coach Brian McLaughlin in the absence of Rory Best and Johann Muller, who were away on Rugby World Cup duty with Ireland and South Africa respectively.
On signing the contract extension, Henry said: "I'm delighted to have signed the extension. It's something you have to think hard about but as far as I'm concerned, I've had an absolute blast in my last couple of seasons at Ulster and this is where I want to be.
"I've dealt with Brian for a long time now since we worked together at Ulster Schools level and I've built up a good relationship with him and the rest of the coaching staff as well.
"I'm very comfortable being here and I get on really well with everybody. It's a really tight-knit group of players and coaches, and it's a great working environment.
"I'm very excited to have got the contract signed and it allows me to concentrate solely on rugby for the next three years.
"In the last couple of years the team have definitely improved and moved forward. Our success last year has really given us motivation to carry that forward and without a doubt I want to win some silverware in my career and that's hopefully where Ulster are moving forward to."
Commenting on Ulster's poor recent run of results in the RaboDirect PRO12, the 27-year-old explained: "We started really well with our first three games and obviously it's very difficult when you lose a certain number of games in-a-row and confidence is down.
"But we've got a lot of internationals coming back from the World Cup, we've got a really exciting team and we've just got to keep our confidence.
"Personally I'm really looking forward to the next run of games and hopefully getting some good results."
Ulster's operations director David Humphreys is delighted that Henry has committed his long term future to the province.
"We are very happy to have secured Chris' services beyond the end of this season until 2014. Over the past couple of years Chris has developed into a key member of the Ulster team and his ability to play in a number of positions across the back row had been invaluable to the squad and the coaching staff," said Humphreys.
"In the modern game, player durability is becoming a vital part of player recruitment and Chris has been consistently available for selection throughout the last few seasons.
"As one of our senior players, Chris has captained the team throughout the World Cup period and we are delighted that he has committed his future to Ulster Rugby."