He helped the club secure promotion in 1992-93 scoring one of York's penalties in the 1993 Playoff Final shootout victory at Wembley over Crewe.
He was also pivotal in York making the Playoff Semi-Finals the following season, although they did not secure promotion, losing 1–0 over two legs to Stockport County.
[citation needed] The following season, also in the League Cup, Pepper played in the York side that defeated Everton 4–3 over two legs.
[6] Pepper made just 15 appearances in league and cup for the club, but failed to find the net, in a period where on-field disciplinary problems haunted him.
At the end of his contract with Aberdeen, Pepper signed for Scunthorpe United on 7 June 2000 where he was immediately installed as club captain.
[8][9] Pepper struggled for over a year to return to full fitness and although he made 1 further substitute appearance for the club he was released at the end of his contract in June 2002.