Naughton played his club hurling with his local Turloughmore club and enjoyed much success. He won a county minor title in the early 1980s before later joining the county senior side. Naughton won his sole senior county title in 1985. This was later converted into a Connacht club title.
Inter-county
Naughton played for Galway at both minor and under-21 levels, however, he had little success. He joined the county senior side in 1986 as Galway faced Cork in a second consecutive All-Ireland final appearance. In spite of Galway being the red-hot favourites, Naughton faced defeat as victory went to the Leesiders on that occasion. In 1987 Naughton won a National Hurling League medal before making another All-Ireland final appearance. That year the men from the West defeated Kilkenny giving Naughton an All-Ireland medal. 1988 saw Galway win a second All-Ireland final, this time with a defeat of Tipperary, giving Naughton a second All-Ireland medal. He added a second National League medal to his collection in 1989; however, a cruciate knee injuryforced Naughton to retire from inter-county hurling in 1992.