The Wales Under-21 cap, now aged 24, made his debut for Wrexham in 2001 and has gone on to establish himself as a first-team regular.
The Hereford-born defender, whose father Mel is the team physio at the Racecourse, formed a good understanding with Wales cap Steve Evans last season.
Pejic's decision increase the options for Dragons boss Brian Carey.
Wrexham signed out of contract Shrewsbury Town centre-back Richard Hope earlier this month.
"There have already been several important signings with Anthony Williams and Michael Proctor returning on a permanent basis, while Eifion Williams and Richard Hope have also joined us," Pejic told the club website.
"As a defender, the addition of the former Shrewsbury captain adds to the manager's options and creates competition for places, which can only be good for the team."
After Wrexham avoided relegation from the Football League on the last day of the season, Pejic is confident that better things are ahead.
"It was a struggle at times last year," he said.
"Happily though we came through a difficult season and now I really do feel that things will get better.
"We showed in the last few games that we can play and it is important we carry on with that improvement.
BBC