The Jefferson School in the area south of Tracy moved at least two times before settling at its present site. The district was formed in June of 1878 and there was a schoolhouse near the town of Carbona until 1895. During this period, the district annexed the Corral Hollow School District that had small attendance but covered a large area in the foothills south of Tracy.
From time to time in the early 1920s, the school was temporarily suspended for lack of students. In 1928 there were so few students attending that the County sold the property to Herman Hilken, who tore down the building and built his home. A year later a school opened on the southeast corner of Linne and Chrisman roads. At this corner several buildings have housed the students. In 1954 the citizens voted for $50,000 bond to enlarge the structure because of the fast growing school population; less than 10 years later, bonds of $200,000 were sold for additions of classrooms and an auditorium. In 1966 the old brick building was structurally brought up to the Field Acts earthquake safety requirements, and new classrooms were added.
* August 2008, facility projects included the installation of a new fire and intrusion alarm system.
* August 2009, a new cafeteria floor was installed.
* September 2009, a new perimeter fence was installed
* 2010, a school facilities bond was passed and new improvements are planned in the near future.
A new school was built on the site starting in 2014. The new school opened in January 2016 and students moved from the sub site to the new building in January 2016. The opening of the school and ribbon cutting ceremony took place in January 2016 where Jefferson School Board members, Jefferson Superintendent, Jefferson administration, Tracy Mayor, DARE Officer, Families and Staff attended and walked the halls.