The original Biloxi Junior High School was built in 1942 on Howard Avenue, across from the present-day Biloxi Community Center. The current junior high school was once “new” Biloxi High School, built in 1961 at a cost of $1.6 million.

In 2002, when the new high school opened north of the Bay of Biloxi, the junior high, serving Grades 8 and 9, moved into the former high school on Father Ryan Avenue.

With the 2009 school year, the ninth-grade class moved to Biloxi High School, and Biloxi Junior High School began serving sixth, seventh, and eighth grade students.

In 2017, the new junior high was opened north of the Bay of Biloxi next to Biloxi High School. Biloxi Junior High serves Grades 7 and 8. The new school is located on Tribe Drive.