2023-2024[5] San Marin High School serves grades 9–12, and offers a comprehensive program of study to approximately 1040 students.

Both of San Marin's STEM programs focus on preparing students for college and career through rigorous, hands-on, project based learning experiences.

Biotechnology Academy enrolls 60 9th graders each year and students are cohorted together for technology of biology, English, and health/college and career readiness during 9th grade.

Among many other awards, the Drama students recently won First Place (Command Performance with perfect score) in the Sacramento State Statewide Lenaea Drama Festival and first places in both Monologue and Scene Category at the Marin Theater Company Scene Fest.

In 2020, the drama department won the bronze award at the Lanaea Theater Festival for its production of "Hard Candy".

Students also attend regional, national and international music festivals and won numerous awards.

Most recently, San Marin Football team won back-to-back North Coast Section championships in 2021 and 2022.

The San Marin Girls Varsity lacrosse team won their first North Coast Section Champion championship in 2024.

During the 1990s and early 2000s, San Marin received significant media coverage locally and nationally for the intolerant behavior of some students and parents.

"[9] Images of this day from the 1987-1988 year book circulated in 2020, drawing shock from students and community members.

[8] In early 1998, a student yelled racial epithets at members of the visiting Tamalpais High School basketball team.

In reaction to the slurs and actions committed by the San Marin High student, parents of four of the black students from Tamalpais filed suit against the Novato Unified School District, charging that a "climate of intolerance" was allowed at San Marin.

[8][11][12][13][14] In the 1998–99 school year, San Marin received widespread media coverage after repeated incidents of hate crimes committed against one of their openly gay students.

He was beaten by three youths off campus on September 15, 1998, soon after forming the Gay-Straight Alliance at San Marin.

Novato's city manager, Rod Wood, referred to "a small group of individuals who are fairly socially maladjusted", who identified themselves as white supremacists and called themselves "the hicks".

[8][15][16][17] The school's behavior code was modified, outlining a range of punishments for racial/ethnic/sexual slurs including reprimand, parental notification, detention on Saturday afternoon, expulsion and police referral.

[14] In 2022, Novato Unified School district led a probe into a group of incidents where San Marin athletes used racial slurs during basketball and football games.