In 1996, a group of dedicated parents and community leaders spearheaded an effort to establish a new middle school with a similar Episcopal educational experience as The Cathedral School, K-6. As a result of this effort, The Cathedral Middle School was established in 1997 as an independent and separately incorporated school.

In the fall of 1998, The Cathedral Middle School opened its doors at a temporary location at the Quapaw Quarter United Methodist Church at 1601 South Louisiana. Shortly thereafter, The Cathedral Middle School Board of Trustees purchased 31 acres at 1701 Cantrell Road to build a middle school with a vision to expand to an upper school. In the fall of 2000, the doors opened for grades six through nine at the newly named Jackson T. Stephens Campus. The campus was named in honor of Jackson T. Stephens for his life-long support of education and his significant role in making The Cathedral Middle School a reality.

The Middle School was dedicated on November 3, 2000. Construction of the Upper School began shortly thereafter and was completed and dedicated on December 7, 2001. In July 2003, the Board of Trustees unanimously voted to change the name of The Cathedral Middle and High Schools to Episcopal Collegiate School to better reflect the heritage, identity, and mission of the School.

On May 11, 2004, Warren A. Stephens, President of the Episcopal Collegiate School Foundation, announced that his father, Jackson T. Stephens, along with he and his wife, Harriet Stephens, President of the Board of Trustees, made a gift of $30 million to establish a permanent endowment for the Episcopal Collegiate School Foundation, which will assure the School's financial security in perpetuity. Additionally, Harriet and Warren Stephens made gifts in 2007 and 2013 during times of important growth for the School.

In December 2006, the Board of Trustees voted to expand the program of Episcopal Collegiate School by constructing and developing a Lower School Division on the Jackson T. Stephens Campus. This exciting new addition to the School provides a cohesive Pre-Kindergarten through 12th grade program on one campus. Episcopal Collegiate School's Lower School Division opened in August 2009.