Saints director of rugby Jim Mallinder confirmed the news following his side's 25-23 defeat at London Irish.
England international Brookes, 25, had surgery on Thursday after suffering an injury against Racing 92 in the European Champions Cup.
"It's a big blow for us as he's been playing well all season and will be out for quite a while," Mallinder said.
Brookes, capped 15 times by his country, joins fellow prop Alex Corbisiero on Northampton's injury list.
Hooker Dylan Hartley did return for Saints at the Madejski Stadium on Boxing Day, lasting 60 minutes in his first appearance since 7 November having recovered from concussion.
Northampton prop Kieran Brookes is set for an extended spell on the sidelines after having an operation on his knee.