The UST Hospital Section of Urology traces its origins to the UST Department of Urology that existed as early as 1933. In 1940, it became the first subspecialty section to be organized under the UST Department of Surgery. The Urology residency training program was also amongst the first to be accredited by the Philippine Board of Urology in 1972. In the year 2017, the University of Santo Tomas Section of Urology Residency Training Program forged a memorandum of agreement with the Chinese General Hospital and Medical Center to improve the training of its residents, which allowed 2nd and 3rd year residents to rotate for 6 months yearly to add more exposure and training. The following year, the Section of Urology started sending two senior residents to undergo further training in Robotic surgery and other state of the art procedures in Severance Hospital, South Korea.

The six-year residency program allows residents to rotate in different areas of the section, supervised and mentored by specialized PUA board-certified urologist, including Uro-Oncology, Trauma, Laparoscopy, PCNL, Endoscopy, Pediatric Urology, Infertility, Female Urology and MRI Fusion Biopsy. Aside from surgical skills training, the residency program also offers weekly and monthly conferences, discussing common, rare and interesting cases, audits and journal clubs. The University of Santo Tomas Hospital Section of urology has produced outstanding graduates, many of whom are well-respected urologists in the local and international community.