The present college of San Juan de Dios Educational Foundation, Inc. was founded on the ideals of nursing and health care, which were pioneered in the Philippines by the Franciscans in 1578. The missionary nursing-like activities were continued by the Daughters of Charity (DC) when the administration of the Hospital de San Juan de Dios was passed on to them in 1868.
In 1913, Hospital de San Juan de Dios opened the first nursing school in the country because of the need to open a school of nursing that will scientifically train students in technical nursing service.
With the opening of the Bachelor of Science in Medical Technology course in 1965, a Liberal Arts course was also opened in the same year. This laid the foundation for the conversion of the school into a College in 1973.
On April 17, 1991, the San Juan de Dios Hospital and College became an educational foundation. It was also during this period when the College began a new baccalaureate course, Bachelor of Science in Physical Therapy, because the desire of SJDEFI administration to address the sensitive needs and the growing demands on medical science.
Because of its mission to continue providing quality education the College of Nursing applied for and received its Level 1 accreditation from the Philippine Accrediting Association of Schools, Colleges and Universities (PAASCU) in 2003.