Brown re-dislocated his right shoulder in the first quarter of the Magpies' gritty eight-point win against West Coast on Saturday at the MCG.
The luckless defender had his arm jammed in an awkward position in an aerial contest with Eagles ruckman Nic Naitanui.
"After meeting with the surgeon today it's been decided he'll have an operation later in the week," Magpies football manager Rodney Eade told Collingwood's website.
"So that will be the rest of the year for him. That will be a 16-week recovery."
The Magpies will also take the opportunity to clean up a niggling knee complaint.
"He'll have a little knee scrape as well, so we'll get that done at the convalescing period," Eade said.
In better news for the Magpies, Jack Frost is expected to be available for Friday night's clash with St Kilda after shaking off the effects of concussion.
The young defender was forced from the field late in the second quarter and didn't return in the second half.
"He's pulled up really well today so fingers crossed he'll be able to play on Friday, but he'll have an assessment and train on Wednesday," Eade said.
Ben Reid would also have been available to play this week, but a bye in the VFL will delay his return by a week.
Reid is yet to play this season after suffering a calf strain in a practice match against Gold Coast on March 2.
Eade said Reid would need one or two weeks at VFL level before being considered for senior selection.
But the Magpies suffered a blow at the lower level, with small defender Ben Sinclair suffering another hamstring injury.
Sinclair strained his hamstring in the Magpies' encounter with the Sydney Swans in round two, but suffered a similar injury in his opposite leg in the VFL on Saturday.
Eade said the Magpies were still trying to determine whether the hamstring issue was muscle or tendon related.
Best case scenario, Sinclair will spend between three to four weeks on the sidelines, while a follow-up scan next week may rule him out for between eight to 10 weeks.
Paul Seedsman, who copped a knock on his knee in the same game, and was sore after the match, will be available for selection.
Seedsman had 11 disposals for the Magpies on Saturday, displaying his run and carry in patches in the game against Geelong at Victoria Park.
Twitter: @AFL_BenGuthrie
