The 19 year old midfielder was stretchered off after Fabrice Muamba's tackle left McCarthy with ankle ligament damage.
The former Hamilton midfielder is now on the road to recovery following an ankle operation that should have added strength to the ankle.
Speaking to the Wigan Evening Post, Roberto Martinez said: "It [the operation] was to make sure the joint remains stable, which will allow his ankle to heal properly.
"The main thing was to make sure it didn't become a chronic problem for him in the future. Ankles are joints that it's easy to not look after properly as you can get through matches. "But he's such a young man that, whatever happens in the next two or three months, we need to ensure he comes back stronger and better for the good of the rest of his career."
McCarthy is now set for a lengthy spell on the sidelines as he undergoes rehabilitation on the injury.