Pejic formed a good partnership at centre back with Steve Evans in 2006–07 with manager Denis Smith saying after beating Scunthorpe United in December 2006, "Scunthorpe have got two of the best strikers outside the Championship and my two centre-backs kept them quiet, they are starting to perform consistently as a pair, so that's good." He made 37 appearances as Wrexham avoided relegation to the Conference Premier on the final day of the season and signed a new two-year contract a month later. He made 22 appearances in 2007–08 as Wrexham were relegated to the Conference Premier. Pejic stayed at the club but rarely featured during the first half of the season and was released, along with Steve Evans, on 2 February 2009.