Chester City

Woodthorpe made his first-team debut for Chester City in the 1985–86 season at Rochdale in the Associate Members' Cup as a 17-year-old apprentice.

The following season saw Woodthorpe make his Football League debut at Bury in a 1–1 draw and he ended the campaign with 30 league starts and two goals to his name. He also found the net in the northern final of the Associate Members' Cup, but Chester lost 2–1 on aggregate to Mansfield Town. He remained a regular in the left-back slot for the remainder of his time at the club and did not miss a game in the 1989–90 season. At the end of the campaign he joined top-flight side Norwich City for a six-figure sum, having made 155 league appearances and scored six times in four years with Chester's first team.

Norwich City

His four years with Norwich included some highlights, such as playing against Inter Milan in a UEFA Cup tie (1993), appearing in an FA Cup semi-final against Sunderland (1992) and scoring in a 3–0 win over Liverpool (1991).

Aberdeen

In 1994, he moved north of the border when he joined Aberdeen for £400,000, again providing matches in European competition. In three years at Pittodrie Woodthorpe made 51 league appearances before returning to the north-west with Stockport County in 1997.

Stockport County

Stockport County had just won promotion to Division One, a level the club would remain at until 2002 when they were relegated and Woodthorpe left on a free transfer, despite captaining the side in his final season at Edgeley Park.

Bury

Woodthorpe joined Bury at the start of the 2002–03 season. His first goal for the Shakers was a local derby winner at Rochdale in the Football League Trophy and his first season ended with Bury reaching the Division Three play-offs.

Woodthorpe remained a regular figure in the Bury defence, despite being 20 years older than some teammates and opponents. Aged 39, he was released by Bury in May 2008.