The HarbourCats were founded in 2012 as an expansion team. On October 12, 2012, the team announced it would be called the HarbourCats after a public naming contest was held that received over 600 submissions.
In 2013, the HarbourCats finished their inaugural season in fourth place in the league's North Division with a record of 22-32.
On September 4, 2012, the HarbourCats announced that Dennis Rogers and Bob Miller would be co-head coaches for the team's inaugural season. Dennis Rogers is also the head coach of the Riverside City College baseball team and Bob Miller holds the same position at Cuesta College. Both coaches will return for the 2014 season.