Moloney, who joined the Cobblers on a permanent deal in February following a loan spell at Sixfields, will need between four and six weeks to recover from his operation.
Town boss Chris Wilder is frustrated by the news after claiming the League Two club were badly advised on how to handle the 26-year-old right-back’s injury.
“Brendan picked up an injury against Burton towards the end of last season,” Wilder told the club’s official website.
“One thing we did say is we didn’t want any injuries lingering on into the new season but we got some bad advice if I’m honest.
“The advice we got was for him just to rest but he’s been to see another knee specialist and he’s been operated on.
“We expect him to be out for between four and six weeks and that is obviously a big blow for us.
“I’m a little bit disappointed in the advice that we got but we have to move on and I’m sure Brendan will rehab pretty quickly and hopefully he’ll be back by the end of August.”