The school was known as Third Street Intermediate School when it first opened in 1911, located on the parking lot of what today is the District Administration Center. In those days Wilson Avenue was called Third Street.

One of the school's first principals was Richardson D. White, as in today's R.D. White Elementary School.  White was later district superintendent.

Originally, Third Street School accommodated only seventh and eighth graders in a two story brick structure with six classrooms and an auditorium. Later, eight classrooms were added.

• In 1913, Third Street was renamed Wilson Avenue by the City of Glendale. Thus, the name of the school was changed accordingly.
• In 1926, the Board of Education decided to rename the campus after former President Woodrow Wilson, who had died two years prior.
• In 1932, a ninth grade was added to the school, prompting a change in title (from "Intermediate School" to "Junior High School") and in location. The student body moved to the campus of Glendale High at Verdugo Road and Broadway (currently where the softball field and tennis courts are located). The former Wilson site became the District Headquarters.

There, Wilson shared the GHS facility for 23 years until a new school was constructed on Monterey Road in 1955 - strictly as a junior high.

• In 1988, Wilson Junior High School earned the CALIFORNIA DISTINGUISHED SCHOOL AWARD from the California Department of Education. This award recognizes the academic achievement and improvement of students. Principal Jim Isenman accepted the award at a special presentation in Sacramento.
• In 1990, Wilson Junior High was re-awarded the CALIFORNIA DISTINGUISHED SCHOOL AWARD for its continuing excellence in academic achievement.
• In 1995, the last ninth grade class was graduated from Wilson Junior High School as the Board of Education moved all ninth graders to the high school campuses.
• In 1996, the name of Wilson Junior High was changed to Wilson Middle School reflecting the fact that the school housed just seventh and eighth graders again.
• In 2002, Wilson Middle School began a "pilot program" of having sixth graders on our campus for the first time in the history of the school 62 sixth graders started that year, and the "pilot" program has lasted ever since.

Wilson underwent a major modernization (Measure K) beginning in February of 2005 and ending in August of 2006. Each classroom had its electrical capacity upgraded. The entire campus was "wired" and connected to the world wide web. Each classroom had its environment updated with brand new heating and air conditioning systems.

• In 2007, Wilson Middle School took on 90 6th Graders from John Marshall Elementary as they went from a K-6 school to a K-5 school. Wilson now has close to 200 6th Graders on the campus.
• In 2008, Wilson Middle School took on 95 plus 6th Graders from R.D. White Elementary as they transitioned from a year-round campus to a traditional calendar campus. Wilson now has close to 300 6th Graders on campus. Wilson's enrollment is close to 1,300 students in 6,7,8th Grades.
• In 2005, 2006, 2007, 2008 was awarded the California Department of Educations' Title 1 Academic Achievement Award. This award is given to schools whose Title 1 students demonstrate improved academic achievement from one year to the next. Principal Richard Lucas accepted the awards from California State School Superintendent Jack O'Connell.

Woodrow Wilson Middle School was 100 years old September 2011. On October 22, 2011 Wilson Celebrated 100 years of educating the youth of Glendale.  Approximately 800 past, current and future Wilson students, alumni, and families shared the day with us.  The 100 Year Video, "Wilson @ 100" was shown to the guests!

April of 2011, the citizens of Glendale passed Measure S.  This bond measure provides $270 Million over the next 30 years to upgrade all of the Glendale Schools technology infrastruction and complete upgrading of school site buildings.

During the Summer of 2012, Wilson's Gym Floor was replaced with a traditional wooden floor.  The previous gym floor was "ruberized".  It was installed in the early 1980's as a result of a broken water pipe that warpped the previous wooden gym floor.

April of 2014 Principal Rich Lucas announced his retirement after 27 years serving as Asst. Principal and Principal.  Dr. Chris Coulter - Principal of Daily High School was appointed as Principal during the Summer of 2014.

January of 2018 Dr. Chris Coulter was appointed to Director of Teaching and Learning and Dr. Narek Kassabian-Principal of RD White Elementary School was named the new Principal at Wilson. In 2024, Dr. Narek Kassabian was promoted to Director of Human Resources at GUSD and Dr. Alen Akhverdyan, a former Wilson Middle School student himself, was appointed principal.