Pejic impressed in a 3–2 win away to Notts County in a Football League Trophy match in September 2004, leading manager Denis Smith to say of him, "Our young central three haven't played together much, but Pejic was immense again, his defensive header in the last minute was worth a goal. He's come on again this season – that's good as we are expecting boys to do men's jobs." It was in this match that Pejic scored his only goal for the club. He featured for Wrexham in the 2005 Football League Trophy Final on 10 April 2005, after coming on as a substitute for Stephen Roberts on 14 minutes, which finished in a 2–0 victory over Southend United after extra time. He made 44 appearances in 2004–05, which saw Wrexham go into administration and relegated to League Two. Pejic missed four months of 2005–06 after tearing cruciate knee ligaments in August 2005 but returned in January 2006, helping Wrexham to the final of the FAW Premier Cup for the second year in succession. He agreed to a one-year extension to his contract in June 2006.