In the 2011-2012 season, the girls Basketball team won San Diego CIF by defeating West Hills High School. Varsity Girls Soccer also won a CIF Div. 2 Championship in 2013. The Serra Football program also has won 5 total league championships, in . 1999, 2004, 2008, 2012, and 2013. They are currently in the City League.
Serra High School's most well-known rival is Patrick Henry High School. The Serra Basketball team and Football team have competed against Patrick Henry's teams every year. The Field Hockey team, however, is most known for having a rivalry with Scripps Ranch High School which is located the Scripps Ranch community of San Diego. The Serra Field Hockey team is among the best high school programs in the nation, accruing dozens of league titles and CIF Championships.