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.
He added a second National League medal to his collection in 1989; however, a cruciate knee injury forced Naughton to retire from inter-county hurling in 1992.