The Shooters were founded as Glen Shields in 1998 as one of the original eight clubs to join the Canadian Soccer League in its inaugural season. The club changed their name to the Glen Shields Sun Devils the following year. They underwent another name change, this time to the Vaughan Sun Devils in 2002 and, after merging with the York Region Shooters in 2003, became the Vaughan Shooters prior to the 2004 season.
With the creation of the new International Division of the Canadian Soccer League, and to celebrate the club's strong Italian heritage, the club changed its name yet again, becoming the Italia Shooters in 2006 until 2010 when it was changed to the present York Region Shooters, reflecting the previous merger in 2003 and the larger area of York Region the club has played in and represents. The club has also introduced new crests over the years, mostly recently updating the crest for the 2011 CSL season.