[1] The franchise was launched by Centerfield Partners of Dublin, California but was sold to Red Sports and Entertainment Group on November 15.

Former Fresno State College World Series champion and local player Steve Detwiler hit two home runs.

[7] San Rafael finished the season 34–26, defeating Maui in the North Division championship series.

[8] Outfielder Maikel Jova was named North American League Most Valuable Player and also held a 37 game hit streak.

On January 14, 2013, it was announced that San Rafael would become charter members of the Pacific Association along with Hawaii, Sonoma County and Maui.

[13] San Rafael opened their season with inter-league play against the Freedom Pro Baseball League of Arizona.

[17] After clinching the first-half Pacific Association title with a 23–16 record, President and GM Mike Shapiro announced manager DiPace left to pursue other baseball opportunities.

[19] In August, Eric Byrnes made his debut, where San Rafael donated a portion of ticket sales to the Pat Tillman foundation.

In August, he was signed by the Lake Elsinore Storm, the High-A affiliate of the San Diego Padres.

[27] On May 16, Derrick Pyles was announced as manager, replacing Kavanaugh who guided the team to two championships in four seasons.

After a 38–26 regular season record, San Rafael defeated Napa and Sonoma, claiming their fourth championship.

San Rafael finished 22–18 in the regular season and defeated the Martinez Sturgeon in the bay championship series.

[30] San Rafael finished with a Pecos League best 41–9 record but were defeated by the Tucson Saguaros in the Pacific Division championship series.

[31] San Rafael finished with a 39–8 record and claimed their first Pecos League championship against Tucson.