He made his first competitive appearance for Inverness on 18 August 2012. During this appearance he scored a late equalising goal in a 2–2 draw against Hearts at Tynecastle.[2] He made an assist in his second match, a 4–2 loss against Celtic. Then scored his second goal for the club in his first start away at Hibernian.
Despite a promising first campaign with Inverness with Terry Butcher, Pepper failed to feature during his second season and was subsequently released by the club in May 2014 by manager John Hughes.[4]
However, Pepper stayed in Scottish football by signing for Greenock Morton.[5] He agreed a new deal with Morton in May 2016.[6] Pepper was part of the team that won the Scottish league One title in his first season at Greenock Morton. Pepper featured in every game up of his second campaign until February 2016 when suffered a knee injury and didn't feature again for the first-team. After 3 seasons with Morton, Pepper left the club in May 2017 at the end of his contract.[7]
After spending 2 years without playing first-team football, still recovering from injury, Pepper moved to Belfast to sign for NIFL Premiership side Glentoran.[8] In his first month as a Glentoran player, Pepper won the Glentoran Supporters Player of the Month Award for August 2018 with 85% of the vote.[9] Pepper was praised by his manager Mick McDermott, who said "I have said it before, and I will say it again, that we have the best two full-backs in the league"[10] After two seasons with Glentoran, Pepper signed for Big Two rivals Linfield.[11]
^Mitchell, Jonathan (15 May 2017). "Player contracts update". gmfc.net. Greenock Morton F.C. Archived from the original on 12 August 2018. Retrieved 15 May 2017.
^"Welcome Conor Pepper". glentoran.com. Glentoran F.C. 2 August 2018. Retrieved 12 August 2018.