The 36-year-old is currently the number two at Old Trafford to David de Gea, but he has been restricted to just two appearances for the Red Devils this season, which both came in the EFL Cup.
Heaton was a notable absentee from the squad against Fulham last time out, having been on the bench for Man United's last 12 Premier League matches.
The goalkeeper has revealed that he 'rolled his ankle' ahead of the FA Cup quarter-final, and he is now facing at least "a couple of weeks" on the sidelines.
"Manchester United will be without goalkeeper Tom Heaton for a few weeks, as he recovers from an ankle injury he picked up prior to the international break," read a statement on the club's official website.
Heaton returned to Old Trafford in 2021, but he has only made three appearances for the Red Devils since his return, and his contract with the club is due to expire at the end of the campaign.
"Yeah, unfortunately the day before the Fulham game, I rolled my ankle in training," Heaton told Man United's official website on Thursday.
"Thankfully, it's not too bad but it'll mean a couple of weeks out, I think. I should be back some point in April somewhere, hopefully halfway through.
"It's an occupational hazard unfortunately, a bit of a random one but, yeah, I just went over on the ankle and nicked the ligament. I'm in this [protective boot] for another few days then hope to get it back moving again."
Heaton's absence means that Jack Butland will provide back-up to De Gea, with the Englishman looking to make his first appearance for the club since arriving on loan from Crystal Palace in January.
However, only an injury to De Gea will open the door for Butland, with Red Devils head coach Erik ten Hag unlikely to rotate his goalkeeper at this stage of the campaign.
There are expected to be major changes in the goalkeeping department at Old Trafford this summer, with Butland, as it stands, set to return to Palace, while Heaton is out of contract at the end of June.
Dean Henderson will return to Man United following a loan spell at Nottingham Forest, but he is then expected to depart on a permanent basis.
The Red Devils also have Nathan Bishop on their books, but the 23-year-old is yet to make a first-team appearance for the club since arriving from Southend United in 2020.