The 19-year-old Ealing Trailfinders second-row/back-row, who head coach Kenny Murray had high hopes for before the tournament, suffered the injury late on in the loss to Wales in round two on February 11.
Scottish Rugby and his club will now work closely together on any operation he needs plus his rehabilitation and Murray said: “He’s got a long-term injury to his knee, so he’s going to be out for at least the rest of the season and probably longer - it could be up to the end of this calendar year.
“It’s a real shame for him. He obviously did well when he was on during the game down in Wales and was really developing well. He’s still learning the game, but showed a lot of potential in the game time he had.
“He’ll get the appropriate medical support and we’ll hopefully get him back on the pitch as soon as we can.”
Ollie Leatherbarrow, who scored two tries in the round one loss versus England, returns to the starting XV after being with Exeter Chiefs a fortnight ago.
He will wear No.8 at The DAM Health Stadium in Edinburgh with Matthew Deehan switching to six in the only change to the starting XV.
Rudi Brown, Tim Brown and Thomas Glendinning are added to the bench.
Scotland under-20s: Robin Mc Clintock; Ross McKnight, Duncan Munn, Andy Stirrat, Ollie Melville; Christian Townsend, Murray Redpath; Michael Jones, Patrick Harrison, Gregor Scougall, Josh Taylor, Max Williamson, Matthew Deehan, Rhys Tait (C), Ollie Leatherbarrow. Subs: Gregor Hiddleston, Ali Rogers, Callum Norrie, Rudi Brown, Tim Brown, Jonty Cope, Euan Cunningham, Thomas Glendinning.