McGinn missed Celtic's trip to Germany to take part in St Pauli's centenary celebrations after going over on his foot in the final training session of the season on Monday.
The 22-year-old then learned he will miss the start of pre-season training after tests confirmed he had broken a metatarsal.
McGinn said. "I will see a specialist on Thursday to see if I need a cast or an operation, or both.
"It's a big blow. It happened during a small game near the end of the session. It was going well until I went over on my foot when I went to hit a shot.
"I knew right away that I had done something wrong and the pain on the outside of my foot got worse.
"The physio said that it looks like a clean break and will heal well, which is encouraging. But I will miss the start of pre-season training and will have to play catch-up.
"I just hope my natural fitness can help me get me back as quickly as possible."
McGinn's mood would no doubt have been lifted later, if only temporarily, when he watched his Northern Ireland team-mate Paddy McCourt light up an end-of-season exercise with a virtuoso effort as Celtic won 2-0 in Germany.
McCourt, who scored spectacular goals after mazy runs against Falkirk and St Mirren this season, collected the ball on the halfway line before beating three men down the touchline and cutting into the penalty box, finishing off by nutmegging the St Pauli goalkeeper and finding the far corner.
Morten Rasmussen turned his man and finished from six yards late in the game to seal a 2-0 victory for a strong Celtic side as Neil Lennon again showed he had instilled a winning mentality in the Celtic side.
Lennon will now wait to see whether he has done enough to land the manager's job on a permanent basis after leading Celtic to victory in eight consecutive Scottish Premier League matches.
Celtic are also waiting to see if their pursuit of Blackburn midfielder Steven Reid will come to fruition amid competition from West Brom, who have held initial talks with the Republic of Ireland midfielder following his two-month loan spell at The Hawthorns.