Clegg arrived at the club little under 12 months ago, replacing Jody Banim in the Hive Arena dugout.
In his first full season at the club, the Blues have found themselves fighting for promotion - thanks in large part to an impressive unbeaten away record in the league.
However, a run of one win, five draws and two defeats in their last eight matches has seen the club drop to fourth in the Northern Premier League table, 10 points behind leaders Radcliffe.
Prior to his time at Rylands, Clegg spent three years in charge of Ashton United and five years with Atherton Collieries before that.
During his time at Colls, the club were promoted three times, earning them a spot at Step 3 football.
On the new deal, Blues chairman Mark Pye said: “We are really pleased to be extending Cleggy’s contract.
"He’s done a fantastic job since joining us last year - not just with the first team, but he’s integrated himself so well within the club as a whole.
"We look forward to much more to come.”
Photo credit: Warrington Rylands