He has made contributions (see e.g.[6]) to the understanding and application of soft systems analysis developed by Peter Checkland at Lancaster University.

In the 1990s, with colleagues Martin Weller and Garry Alexander, Naughton created the university's first major online course (You, your computer and the Net) which attracted 12,000 students per presentation in its early days and marked the beginning of the university's rise as a major provider of online education.

In 2001 he set up the university's Relevant Knowledge programme—a suite of short online courses on topical technological issues and was director of the programme until 2009.

In collaboration with Professor Sir Richard Evans and Dr David Runciman, Naughton is a principal investigator on a five-year research project on 'Conspiracy and Democracy' funded by the Leverhulme Trust.

[1] Archived 8 December 2015 at the Wayback Machine Both projects are based in CRASSH (the Centre for Research in the Arts, Social Sciences, and Humanities) at Cambridge University.

In the early 1970s, Naughton wrote for the political and cultural weekly, the New Statesman, mainly covering scientific issues.