The 26-year-old, injured in Sunday's McKenna Cup defeat by Cavan, will need surgery followed by a lengthy recovery and rehabilitation process.
McAliskey had scans at the Ulster Clinic in Belfast on Monday.
The loss of McAliskey, a renowned finisher, is a serious blow to Tyrone's prospects for the forthcoming season.
He was the Red Hands' top scorer in the 1-13 to 0-12 loss to the Breffni men at the weekend with five points, before suffering the injury to his left knee in the 62nd minute.
Apart from Tyrone's first defeat in the competition in six seasons, Sunday's reversal came at a heavy cost in terms of injuries.
Michael Cassidy suffered a hamstring injury just 15 minutes into his debut, while Rory Brennan and Ronan O'Neill also picked up knocks which could rule them out of next weekend's meeting with Ulster University at Healy Park.
Tyrone must win their remaining games against UU and Donegal to have any hope of reaching the McKenna Cup semi-finals.
Their chances of winning the title for a sixth successive season have suffered a further setback with All-Star Mattie Donnelly being suspended following a straight red card in the closing stages of Sunday's game.
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Tyrone attacker Connor McAliskey has been ruled out of the entire 2017 season after suffering a ruptured cruciate ligament injury.