Besides the regular four-year program, San Juan Bautista School of Medicine offers a five-year program. This program provides the opportunity to extend to three years the Basic Sciences. It has been a successful plan, in providing students during their first year, with more time to assimilate knowledge. This program combines first and second year courses, while maintaining a coherent and logical sequence. The students may opt for this program at the time of entering the School, or during their first year of studies.

The five-year program curriculum scheme is the same as the regular program. It works only with the Basic Sciences courses. It is designed by semesters and courses do not overlap. It is allowed to repeat only one (1) year, for justifiable reasons, in any of the two programs.