Rizal first studied under Justiniano Aquino Cruz in Biñan, Laguna before he was sent to Manila. As to his father's request, he took the entrance examination in Colegio de San Juan de Letran and studied there for almost three months. The Dominican Friars asked him to transfer to another school due to his radical and bold questions. He then enrolled at the Ateneo Municipal de Manila and graduated as one of the nine students in his class declared sobresaliente or outstanding. He continued his education at the Ateneo Municipal de Manila to obtain a land surveyor and assessor's degree, and at the same time at the University of Santo Tomas where he did take up a preparatory course in law.

Upon learning that his mother was going blind, he decided to study medicine specializing in ophthalmology at the University of Santo Tomas Faculty of Medicine and Surgery. Without his parents' knowledge and consent, but secretly supported by his brother Paciano, he traveled alone to Europe, to Madrid, Spain in May 1882 and studied medicine at the Universidad Central de Madrid where he earned the degree, Licentiate in Medicine. His education continued at the University of Paris and the University of Heidelberg where he earned a second doctorate. In Berlin he was inducted as a member of the Berlin Ethnological Society and the Berlin Anthropological Society under the patronage of the famous pathologistRudolf Virchow. Following custom, he delivered an address in German in April 1887 before the anthropological society on the orthography and structure of the Tagalog language. He left Heidelberg a poem, "A las flores del Heidelberg," which was both an evocation and a prayer for the welfare of his native land and the unification of common values between East and West. At Heidelberg, the 25-year-old Rizal, completed in 1887 his eye specialization under the renowned professor, Otto Becker. There he used the newly invented ophthalmoscope (invented by Hermann von Helmholtz) to later operate on his own mother's eye. From Heidelberg, Rizal wrote his parents: “I spend half of the day in the study of German and the other half, in the diseases of the eye. Twice a week, I go to the bierbrauerie, or beerhall, to speak German with my student friends.” He lived in a Karlstraße boarding house then moved to Ludwigsplatz. There, he met Reverend Karl Ullmer and stayed with them in Wilhelmsfeld, where he wrote the last few chapters of "Noli Me Tangere". A plaque marks the Heidelberg building where he trained with Professor Becker, while in Wilhemsfeld, a smaller version of the Rizal Park with his bronze statue stands and the street where he lived was also renamed after him. A sandstone fountain in Pastor Ullmer’s house garden where Rizal lived in Wilhelmsfeld, stands.