A USL Second Division side since their inception in 1996, the Phantoms have regularly made the postseason, missing only twice since their inaugural campaign and posting .500 or better records in eight of their first 10 seasons.

The club posted a mark of 12-6 in their third season and advanced to the championship game before suffering defeat in a 3-2 overtime decision.

The club also launched the W-League New Hampshire Lady Phantoms in 1998 and developed a Super Y-League program in 2003.