The Master of Science in Applied Physics (Medical Physics) program is a two-year program which offers qualified students, particularly those with backgrounds in physics, applied physics, and engineering, the opportunity to do graduate course work and research in the applications of the concepts and methods of physics to the diagnosis and treatment of human disease.

Graduates of the proposed MS Applied Physics (Medical Physics) program are eligible to undertake a clinical residency leading to board certification in three specialty areas namely: radiation oncology medical physics, diagnostic radiology medical physics, and nuclear medicine medical physics. The clinical residency and board certification is done by the Society of Medical Physicists in the Republic of the Philippines (SMPRP).