Off-contract at the conclusion of this campaign, the 28-year-old inked a new deal with the club to end any hope of him joining the PNG Chiefs or Perth Bears' inaugural rosters.
Cowboys and Queensland halfback Tom Dearden is tied down to the club until the end of the 2029 season.
Having debuted in 2018 for his boyhood club, Clifford enjoyed stints at the Newcastle Knights and in England's Super League before returning to Townsville in 2024.
He's made a strong start to this season, helping Todd Payten's side spring into the competition's top six, registering four tries and assisting a further seven.
"This decision was a no-brainer for my family and me. This is our home here, and I'm really excited with what this playing group has been building this year," Clifford said.
"The Cowboys mean everything to me. I've been supporting this club since I was a little boy in Tully.
"To be able to put the Cowboys jersey on for at least the next two years and represent the region and my family is something I look forward to every single week."
Clifford was made to work for his latest deal, with 22-year-old Tom Duffy also in the mix to become one of North Queensland's first-choice halves.
Duffy's move to Brisbane ahead of this season opened the door for Clifford, and he'll look to celebrate re-signing with a victory against Parramatta on Friday night.
Young gun Jaxon Purdue was also in the running, but has since been moved to the centres.
"Jake was challenged in the pre-season to win his spot; he did that and has gone on to play some of the best football of his career," Cowboys chief executive Michael Luck said.
"The partnership between Jake and Tom Dearden in the halves has blossomed over the past 12 months, and we believe they complement each other well."
North Queensland will look to claim their seventh victory in eight games, with lock Jason Taumalolo set to overtake Johnathan Thurston (294 games) against the Eels as the most-capped Cowboys player.
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