Brown was playing his first match back in the seniors last Saturday against West Coast after originally dislocating his shoulder during the club's Round 2 win over Sydney.
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Brown had played three matches in the VFL but had been promoted back to the senior side at the expense of Lachlan Keeffe, who endured a torrid match against Adelaide's Josh Jenkins the week before.
But Brown's return didn't even last a quarter as he re-injured the shoulder in a marking contest just before quarter-time as Eagles' big man Nic Naitanui launched himself at the pack.
Brown was subbed off at the first change and sent to hospital, but after viewing more scans on Monday, Collingwood have opted to send the 25-year-old for surgery.
The injury means Collingwood's key defensive stocks are somewhat limited and the club will have to make do with youngsters Jack Frost and Keeffe until Ben Reid returns from a calf injury.
Ben Sinclair also looks likely to spend time on the sidelines after injuring his hamstring in the VFL on the weekend, although the club are confident Paul Seedsman will be fit to play despite suffering a knock to his knee in the twos.