In the fall of 1959, San Jacinto Junior High opened its doors at 3102 San Augustine to 850 students in grades seven through nine. The school was named San Jacinto because of the history covering the area where the building stands. Lonnie B. Keller was the first principal and the faculty was made up of 45 teachers. From 1959 to 1965, San Jacinto had a vocational program, as did all Pasadena ISD junior high schools. In the fall of 1963, Ralph Stafford became principal. In 1968, intermediate schools became a new innovation in Pasadena ISD. San Jacinto Intermediate was formed and began serving students in grades sixth through eighth. In 1976, 1,005 students were enrolled at the school. 

In the late 1990s, renovations were made to the campus. A science wing, library, office and a lounge were added to the campus. As time went on, the need for a new building for San Jacinto Intermediate became clear. The science department appeared to be sinking and pulling apart from the building. When it rained, the building leaked and experienced some flooding. In 2008, San Jacinto relocated to a new building on 3600 Red Bluff Road in Pasadena. 

In recent years, San Jacinto was the first intermediate school to provide one-to-one technology for students in the district.  It was also one of the first intermediate schools to institute school-wide Personalized Learning.  The school also hosts one of the largest junior high basketball tournaments in the state for both girls and boys. San Jacinto currently serves around 670 students in seventh and eighth grades.

List of Principals

• Lonnie Keller 1959-1965
• Ralph Stafford 1965-1971
• George Crowson 1971-1974
• James Nutt 1974-1984
• David Post 1984-2006
• Dianna Walker 2006-2018
• Diane Phelan 2018-2023
• Travis Regnar 2023-Present