He was first elected in 1997, beating Norman Lamont, the former Chancellor of the Exchequer, and in May 2007 announced his decision to step down as an MP at the next general election, although he said that he would have stood again if a snap election had been called. From 1999 to 2005, Willis was the Liberal Democrat Shadow Education and Skills Secretary, having previously served as Higher Education spokesman and acting spokesman on Northern Ireland. Following the 2005 general election, he was appointed chair of the House of CommonsScience and Technology Committee, succeeding Labour's Ian Gibson. In 2006, he stated that he would force an election for the party leadership by standing if there would otherwise be only one candidate. As two further candidates came forward to challenge the eventual winner, Sir Menzies Campbell, Willis did not stand. Campbell's victory left a vacancy for the post of deputy leader. Willis considered running in the deputy leadership election but did not submit a nomination. At the Liberal Democrat Federal Conference in Spring 2007 he proposed a change to official Liberal Democrat policy on the future of Trident in an amendment to commit the party to getting rid of Britain's nuclear deterrent. The amendment was opposed by the party leadership and, in one of the closest votes in recent years at a Federal Conference, the amendment was defeated by 454 votes to 414. In September 2008, Mr Willis provoked the resignation of Professor Michael Reiss from his position as Director of Education at the Royal Society. Professor Reiss, in a speech to the British Association for the Advancement of Science, had commented that in his experience as a teacher, children with creationist views were difficult to persuade otherwise, and that merely silencing them didn't cause them to change their minds at all. He suggested an alternative approach: that such pupils should be allowed to express their opinions, not as science, but as 'a world view'. This would provide the opportunity for real discussion and science teaching. Willis demanded action by the Royal Society against Professor Reiss, so stimulating a furore which concluded with Reiss' resignation on 17 September.
He is a keen supporter of Burnley Football Club. He married Heather Sellars in 1974 in Staincliffe. They have a daughter Rachel and a son. His daughter Rachel is a television personality best known for her role of Connie, the so-called "AOL lady" in the AOL adverts, a role which she played from 1998–2003. Although from Burnley, he has lived in the Yorkshire area for many years.