After helping Barnet to the Conference title in 1990–91, he was signed to Wimbledon, a Football League side, at the relatively late age of 23.
He made a huge impression at Underhill over the next eighteen months and was named as the club's Player of the Year for 1990.
At the end of the season, Barry Fry led the "Bees" to promotion to the Football League as champions of the Conference.
Clarke was immediately thrown into the first team at Plough Lane, playing 12 league games and scoring three goals as the "Dons" finished seventh in the First Division.
The club then became founder members of the Premier League, posting a 12th-place finish in 1992–93; Clarke scored five goals in 33 appearances.
Despite being forced to play their home games at Crystal Palace's Selhurst Park, they rose to sixth in 1993–94, finishing higher than all London clubs except Arsenal.
Clarke started the 1998–99 campaign on loan at First Division side Port Vale but made just six goalless appearances for John Rudge's "Valiants".
He rediscovered his scoring form at London Road under Barry Fry, his former manager at Barnet, bagging 18 goals in 43 appearances in 1999–2000.