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.
The Victoria Harbourcats went 25-29 in their 2nd season of play in the WCL. Victoria set the record for the most at-bats by a whole team having 1937 at bats in just one season. Victoria drew 45,571 fans through the gates in 30 home games, averging about 1,519 fans a night. This put Victoria second in WCL attendance in the 2014 season.
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.