Manhattan High School at The Beacon School was created in 2015 by veteran principals Marta Barnett and Ruth Lacey to coincide with the opening of The Beacon School's new building. The program was created to provide standardized assessment students with social and emotional disabilities a place to grow academically in the least restrictive environment possible. About a quarter of P35M students attend inclusion classes with Beacon School students, some full time. Approximately the same number of Beacon School students receive special education services provided by P35M. Students are given new opportunities throughout their high school experience to participate in the general education environment to the extent their disability allows.
Manhattan High School students at The Beacon School follow the standard New York State High School curriculum, culminating in Regents exams every January, June, and August. Students have options to take a variety of courses in the maths and sciences, beyond the minimum required for a Local or Regents Diploma. In addition, students participate in many different engaging elective courses, which rotate every semester. There are also after school programs, including night classes, clubs, and teams together with Beacon School students.