El Capitan opened in 2013 and is the 6th comprehensive high school in the Merced Union High School District. The class of 2016 was the school's first graduating class. The class of 2017 will be the first class to spend all 4 years at ECHS. Located in northern Merced the school serves both the north and south sides of the city.

El Capitan is the second school to bear that name. The original El Capitan was open from 1959-1962 and was located on the current Merced High School campus. In 1962 El Capitan and Merced High were combined into one school. 51 years later MUHSD named its newest school to honor the original campus and the alumni of that school.