McGoldrick will undergo surgery on the injury that was initially suffered in February, and McCarthy has admitted that the club's main focus is to have the forward return for the start of next season.
The 55-year-old is quoted by BBC Sport as saying: "He's having an operation on Thursday on his cartilage, which he damaged this week.
"We'll now just get him ready for the start of the season. It's a shame because he had worked ever so hard."
The 26-year-old has netted 16 times in 34 appearances for the Tractor Boys this season.