The 20-year-old has rejected offers from the Aviva Premiership and rival Welsh regions, Press Association understands.
Former Wales Under-20s captain Jenkins has signed the new deal while the club rugby civil war rages on.
The four regional sides and the Welsh Rugby Union remain at loggerheads over the future of the domestic game.
Wales captain Sam Warburton has signed a pioneering WRU central contract, but it remains unclear where he will play his rugby next season.
Blues rugby director Phil Davies admitted it is important to keep securing new deals for talented emerging players, despite continued unrest.
"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," Davies told Cardiff Blues' official website.
"Ellis is 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.
"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."
Jenkins captained Wales Under-20s to the final of the Junior World Championships last summer, and skippered Cardiff for the first time in their LV=Cup clash at Bath last weekend.
Admitting it was a straightforward decision to sign a new deal, Jenkins said: "I've been at the Blues since I was 14 and grown up with many of my current team-mates.
"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."
- Sports & Recreation
- Cardiff Blues
- Phil Davies
- Aviva Premiership