McNaughton is a 1994 graduate of LeMars High School. McNaughton went on to play baseball at the University of South Dakota, where he graduated in 1999. McNaughton's amateur baseball career began with the Akron Rebels in 1995-1996. In 1997, McNaughton joined the Vermillion Red Sox, where he played until 2002. McNaughton rejoined the team in 2004 and continues to play infield and outfield for the Red Sox. McNaughton was a member of the 2004 Class "B" State Champion Red Sox team. McNaughton was also was a member of the 2006 Class A State Champion Vermillion Red Sox. In 2009, McNaughton will be playing his 15th Season of Amateur Baseball, and his 13th Season with the Red Sox.