In the spring of 2003, two NISD programs, Challenge High School and Sunset High School combined to create a new school that would be more responsive, efficient and accommodating to the needs of students who are not thriving in the traditional, comprehensive high schools. This new school built a firm foundation based on the best practices from Challenge High School and Sunset High School where students could engage in effectively designed, relevant curriculum and a unique schedule in order to earn a Texas high school diploma. Northside Excel Academy was established to serve seniors from throughout the Northside Independent School District who have experienced a "disconnect" from traditional education.

The students who last attended Challenge High School and Sunset High School participated in the naming of the new school. Of the three proposed names put forward by the students, The Northside Board of Trustees chose the name Northside Excel Academy.  The name seemed fitting because of Northside's commitment to excellence and their desire for all students to have a learning community where students can excel.