The 20-year-old made his full debut for the region in both the Heineken Cup and RaboDirect PRO12 and was named captain when Blues faced Bath in the LV=Cup last weekend.
Director of Rugby Phil Davies described Jenkin's signature as a real statement of intent for the future.
"At Cardiff Blues we have some of the brightest young back row players in Welsh rugby, so the news that Ellis has agreed a new contract is absolutely fantastic," he said.
"Ellis is the former Under-20 captain for Wales and a very mature and intelligent young player, especially at the breakdown where he makes good decisions.
"He is a big talent and someone who will only get better. Ellis wants to develop as a number seven and also has the ability to play six. We are lucky to have the likes of him, Josh Navidi and Rory Watts-Jones in that position.
"We're pleased that we've retained his services because he would have undoubtedly attracted the attention of other clubs. But he wants to remain a Blues player and help this region get even stronger."
CEO Richard Holland added: "Ellis will be a huge asset to our region for years to come and is exactly the type of player who we see as the future of the Blues.
"Ellis is an extremely talented flanker and proven leader, a fact that shone through at both the Junior World Championships and when he led the Blues for the very first time at Bath last weekend.
"This is a very positive signing for us, which I know will please our supporters at this important time for our region. We're determined to continue to strengthen the squad and plan to make more important announcements in the coming weeks."
Jenkins played for all the Blues age grades and won the Welsh Championship every year he was in the squad. His performances saw him promoted to captain the Blues Under-18 squad and then on to Wales.
He was integral to the Under-20 Junior World Cup team in South Africa in 2011/12, that were the first team to beat New Zealand at that level, earning a spot in the semi-final.
Jenkins said: "I've been at the Blues since I was 14 and grown up with many of my current team-mates. I've enjoyed my development here and I always wanted to remain a Blue.
"To captain the Blues last week was a huge honour and now I want to establish myself as a regional player. I've been involved the last few months and I'm hoping next season I can really kick on.
"I enjoy the environment here, believe in the coaching staff we have in place and it's great to sign and now concentrate on the rest of this season. We still have a lot to play for and I want to feature as much as I can and get even more experience at this level."