Bothroyd was a mainstay for Perugia during their 2003–04 season, competing in the majority of their league matches, but he was unsettled in Italy. He joined Blackburn Rovers in August 2004 on loan from Perugia. After getting sent off against Norwich City for violent conduct, after kicking opposing midfielder Mattias Jonson, he was unable to cement a place in the first team and returned to Perugia at the end of the season. He did manage to score once in the league for Blackburn, during a 2–2 draw with Liverpool in October 2004. In 2008, Bothroyd held an interview with the "South Wales Echo" where he revealed that he, along with other teammates, was the subject of regular racist abuse while playing in Italy.