Harper played for Edinburgh junior team Hutchison Vale before being recruited by Hibernian and making his professional debut at the age of 17. Harper was a member of a small minority in Scottish football as a black footballer. He joined English club Sunderland as a youngster but only made one appearance for their first team. He later had spells with St Johnstone, Dundee and Brechin City before returning to Scotland with Airdrieonians and then Raith Rovers. In 2001, he moved back to England to sign for Bradford City but was released after just one season. After a brief spell with Cowdenbeath, Harper returned to Scotland with Hamilton Academical before ending his career with East Fife. Harper won two caps for the Scotland national football team in 1999. He made his international debut in a 1-0 win over Northern Ireland on 8 February 1999 and scored his only goal for Scotland in a 2-1 defeat to England on 15 March 1999. He played in both matches as Scotland finished third at the 1999 UEFA European Football Championship. After retiring from playing Harper became an assistant coach at Hamilton Academical and also worked with the under-18s and under-20s teams at Sunderland. He was appointed manager of National League side Hartlepool United in October 2015 but was sacked four months later after failing to lead them out of relegation trouble.