Despite not playing since April, Fagerson was named in the initial British & Irish Lions squad before a calf problem resurfaced and he was forced to withdraw before the party headed to Australia.
Scotland considered taking him on their summer trip to New Zealand and Fiji but it was decided Fagerson would be better off recovering at home.
However, head coach Franco Smith revealed Fagerson was due to see a specialist on Friday.
"Zander has had a bit of a setback in the gym regarding a knee injury," Smith explained to Scotland Rugby News. "He's also seeing a specialist to make sure that we follow a good rehabilitation programme from that perspective. It's a different injury than he struggled with. It's not his calf, it's a knee injury. We will hopefully get him back in time."
Smith also revealed Huw Jones is also due to seek specialist advice when he returns to the club on Monday.
Jones spent two months on the sidelines after the Six Nations earlier this year with an Achilles injury before returning for the last two games of the URC regular season.
Jones then missed Glasgow's quarter-final against the Stormers and a semi-final against Leinster. At the time Smith said it was an issue Jones would need to manage "for the rest of his career".
Jones recovered in time for the Lions tour starting six matches including all three Tests against the Wallabies.
"Huw is going to come back in with an injury that needs to be resolved and managed," said Smith. "We will have more clarity regarding that early next week. He has already seen a specialist around that, so we will see what the outcome of that is."
Another Lion, Sione Tuipulotu, is expected to have recovered from the hamstring injury which affected his participation in the latter stages of the tour to Australia.
Tuipulotu was sidelined with a pec injury for four months from mid-January to mid-May, missing the whole Six Nations, before returning for Glasgow's final regular-season game at Leinster and their two URC knockout games before joining up with the Lions.
"Sione has declared himself fit," said Smith. "He's only back from Australia today, I think. It'll be good to have him back and he'll be freshened up. We will obviously then follow due process to make sure that his return to performance is done properly. His integration into the group in the next three weeks is going to be important."
The other member of Glasgow's Lions contingent, Scott Cummings, will return to the club "healthy" on Monday, with all three having been given a five-week break following their Lions exertions.
Smith said he was not unduly concerned about the workload on Jones, Tuipulotu and Cummings - who also missed three months of last season after suffering a broken forearm in January.
"The difference with our Lions that were out there is that they didn't play much for us leading up to the Lions tour," he noted. "Since the Six Nations or, in the case of Sione, even before that, they weren't much available to play rugby.
"There was a lot of rehabilitation and a lot of training to get them better. They've had some good breaks, but their number of minutes on the pitch was actually quite reduced in comparison to even the other internationals that we have in our group. So they were the only group that's had five consecutive weeks of rest now, which is ideal.
"We're going to try and manage them in such a way that they go into the Scotland environment in November with three clear objectives. One, to be physically at top level. Two, to have enough rugby minutes under their belt to make a difference for Scotland in the internationals. And three, to contribute to Glasgow Warriors and to progress our aspirations.
"Our ingredients are enthusiasm, creativity and energy. So to fill those stores takes a bit of planning and skill. And we're going to hopefully allow them to have those ingredients and to achieve those three objectives.
"We would like to have all of those boys not just fit - fit is one thing, it's to be performing - by the time they reach the Autumn Nation Series."