The 21-year-old re-fractured his right foot last week following a knock at training.
Dean was limited to two VFL appearances last season due to two separate injuries on the same foot.
“We are disappointed for Charlie who has had unfortunate luck with his foot over the past year,” Collingwood General Manager of Football Graham Wright said.
“While Charlie is an extremely resilient footballer, we empathise with him after being so dedicated during a lengthy rehab last season and over the summer break.
“Our program will wrap our arms around Charlie and ensure he is well supported as he recovers.”
Dean, together with the Club, will consult with a specialist before determining next steps.