Delaney had surgery on the same toe late last year after injuring it against Melbourne in round 18, but has continued to be troubled by it since.
The 22-year-old finally returned in the VFL with North Ballarat four weeks ago, coming on after half-time and playing the final two quarters.
But Delaney pulled up so sore after the match that he struggled to walk for a few days afterwards.
North football director Geoff Walsh told AFL.com.au two weeks ago that the club was seeking "a third opinion" from a medical specialist in the hope Delaney could avoid surgery.
But the Roos announced on NMFC.com.au on Wednesday night that Delaney had decided to have surgery.
Delaney said he thought he had been on the verge of overcoming his lingering toe problems at times this year, but committing to surgery had given him "piece of mind" that he could finally do so.
"I can look forward to having a strong pre-season and come back for next year," Delaney said.
"I'm pretty keen to get it right and give myself the best opportunity and the best chance to have a good year next year."
Delaney has played just six games since North took him with pick No. 69 in the 2010 NAB AFL Draft.
He played five of those games in the first 10 rounds of his second season, 2012, but injury has not been kind to him since.
Hip problems troubled him early in 2013 and, after working his way back to form and fitness in the VFL, he suffered his toe injury in his first game back in the North senior team.
Delaney had a game-high 12 marks (four contested) against the Demons in that round 18 game.
North's faith in Delaney was underlined late in August 2012, when it signed the then second-year player to the end of 2015.
