The former West Coast co-captain had just started to find form in his first year in Queensland, before breaking his foot late in Sunday's win against Adelaide.
With Allen sidelined, versatile teenage big man Cody Curtin will make his AFL debut in Saturday's clash with Essendon at Marvel Stadium.
Taken with pick 43, Curtin - the younger brother of Adelaide's Dan - stands at 200cm and will slot into the forward line and help out in the ruck.
"Cody would have debuted in Round Zero had he not got injured in the last practice game against the Gold Coast Suns," Fagan told reporters on Thursday.
"We don't expect the world from him, but as long as he makes a contest and plays to his strengths, he'll help our team."
Brisbane's run to premiership glory started amid injury carnage in May 2024, forced to call on untried youngsters and shuffle their on-field mix.
Logan Morris famously debuted against the Suns after stuffing himself full of McDonald's following a VFL match earlier in the day.
Two years on, Morris is a dual premiership winner with 90 goals from 51 games.
Ty Gallop, who played in last year's grand final win as a teenage key forward, has had success in shifting to defence following a shoulder injury to premiership teammate Darcy Gardiner in round three.
"The positive thing is he'll (Allen) be back before the end of the year. It could have been worse," Fagan said.
"Funnily enough, injuries have treated us kindly over the last couple of years.
"We've discovered other things about ourselves we may never have known. Logan Morris being one of those.
"We're disappointed for Oscar, but positive we'll keep moving forward as a team."
Sitting fifth with a 4-3 record, the Lions regain star veteran Dayne Zorko following two weeks out with a calf injury, with James Tunstill dropped.
Recruit Sam Draper, who left Essendon as a free agent during last year's trade period, is set to face off against his former club for the first time.
The Bombers have rested Darcy Parish and dropped fellow midfielder Elijah Tsatas after losing Isaac Kako and Archie May to injury.
Former first-round draft pick Nik Cox will play his first AFL game in 630 days after fears concussion could end his career, while Essendon have also recalled Jade Gresham, Max Kondogiannis and Jayden Nguyen.
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