A continuum of education had existed in what is now the City of Milpitas since the Spanish colonial era, only to be interrupted by brief periods from 1848 to 1858 upon the secularization of the Californian missions, and 1954–1959, in which James Lick High School in the nearby city of San Jose became the high school for Milpitas residents.

In 1997 the Boys Varsity Basketball team won the first CCS Division 1 Championship in school history by defeating Oak Grove 44-43.

On December 2, 2006, the Milpitas High School Varsity football team won the CCS Championship for the first time.

The 2008 football season was a successful one for the trojans becoming the De Anza division league champions with a record of 9 and 1.

In 2007, Milpitas High School's varsity girls track & field claimed 3rd place in the overall team title.

In 2004, varsity girls cross country won the team CCS title and qualified for state championships.

These Trojans were one of the few Cinderella story teams that shocked CCS baseball with their outstanding run to the semi-finals.

In 2019, The marching band qualified for finals at the WBA 4A/5A Grand Championships for the first time in school history.

Since 2002, the MHS Symphony Orchestra has provided an opportunity for string musicians to perform a variety of classical and contemporary orchestral literature.

Each year, Milpitas NJROTC hosts "Legions of Troy", a drill meet and athletic competition that many other Californian JROTC units attend.

Weekly lesson plans includes academic instruction, uniform inspection, physical training, and drill.

Students in the class use Adobe InDesign on the computers provided in the classroom to design page layouts for each new issue.

The Milpitas High School's Science Olympiad is a student-run and staff-supported organization that started in 2007 with only a few students.