Bronx Prep opened its doors in 2000 with its inaugural class of 100 5th and 6th graders. As one of fourteen schools chartered by the SUNY Charter Schools Institute out of ninety applicants in 1999, Bronx Prep was one of the first schools to be re-chartered for a full five-year term in 2004. In 2004 the school moved to the building which formerly occupied Junior High School 149 on 149th St. and Willis Avenue. Bronx Prep reached capacity of 700-800 students in grades 5-12 by 2011.