In 1998, the seventh Bishop of the Sioux Falls Diocese, Robert J. Carlson, along with the SFCS School Board, established the first centralized Catholic junior high in Sioux Falls. Prior to this time, students at the junior high level held classes at the former Cathedral High School (converted to a Catholic junior high school in 1961) and at St. Mary School. O’Gorman Junior High would now occupy the former minor seminary building to the west of O’Gorman High School. With extensive remodeling, many improvements were made to suit the 400 students who would now be attending O’Gorman Junior High School. A multipurpose room (gymnasium), locker rooms, and a music room were also added. The first principal to serve at O’Gorman Junior High was Mrs. Colly Broveleit.
In 2019, O'Gorman Junior High School was named as a National Blue Ribbon School, the highest award a school can earn. To date, the school is the only stand-alone middle school/junior high in South Dakota history to have achieved this distinction.