The school has undergone many changes over the century. It was built in 1929 as Harlingen High School. The school later became a freshman only campus. When the freshmen joined high school, Vernon housed only eighth graders.
At the beginning of the '90s, Vernon became one of three junior highs in Harlingen which educated seventh and eighth grade students.
The 1997-98 school year was the first year sixth graders joined the seventh and eighth graders attending the, now, Vernon Middle School.