In 1995, he resigned from Hat Trick and returned to the BBC as BBC Television's Head of Comedy, requesting his contract stipulated "his continued role as a programme producer," as well as overseeing the department. He stayed in this role until 2001, growing increasingly dissatisfied at "official BBC snootiness about comedy".
Perkins meticulously read 30 new scripts every week, but "found himself culturally marginalised at the BBC," saying: "Unfortunately, the term sitcom implies a great disdain. People say it with a curl of their lips." Under Director-General John Birt, Perkins also felt "hamstrung by the inevitable bureaucracy," which not only hindered programme-making, but saw Perkins spending "more time on budgets" than more creative pursuits.
Perkins felt that the changes in how the BBC was run,
(They) set the people that produce programmes in direct opposition to the people responsible for actually paying for and broadcasting them.
There have been occasions when you say, 'Let's just make a deal', knowing everyone is unhappy; where no one gets the budget they want to make their programme. There are people who are inspired by that, but I'm not one of them.