Manuel A. Roxas High School is one of the six schools in Manila to provide the Special Science course for selected individuals at every junior high school level. This program aims to develop mathematical abilities, science skills, and English proficiency of the students through the use of special additional subjects like Information and Communication Technology, Environmental Science, Research, Electronics, and Special Mathematics.

The regular class of Manuel A. Roxas Junior High School offers the approved four-year secondary curriculum of the Department of Education (Dep-Ed). This curriculum includes the education of compulsory core subjects together with the Technology and Livelihood Education (TLE) that includes the subjects like Agri-fishery Arts, Home Economics, Information and Communication Technology, and Industrial Arts, that not only enhances the academic skills of the learners but also develop the basic life skills and technical skills that will form them into a productive member of the society.