A pacy winger, Parkinson began as a Liverpool trainee, winning the FA Youth Cup in 1996, but was released shortly after. He signed for Tranmere Rovers who were managed by former Liverpool striker John Aldridge. He was handed his professional debut on 22 October 1997 when he came on as an 81st-minute substitute for John Morrisey in a 2–1 defeat against Wolverhampton Wanderers. Parkinson settled into Rovers first team squad with the club plying their trade in the second tier of English football. During 2000 and 2001 he featured in two cup runs, which eventually saw him play a part in the 2000 Football League Cup Final, where Tranmere lost out to Leicester City in the final at Wembley Stadium. He memorably scored twice, including a last minute winner in extra time, to help Tranmere knock Premier League side Leeds United out of the 2000–01 Football League Cup. He played his final game for the club on 22 March 2003 against Peterborough United before departing Prenton Park at the end of the 2002–2003 season.