Born in Trozo, Tondo, Manila. Jacinto was the son of Mariano Jacinto and Josefa Dizon. His father died shortly after Jacinto was born, forcing his mother to send him to his uncle, Don José Dizon, so that he might have a better standard of living.

Jacinto was fluent in both Spanish and Tagalog, but preferred to speak in Spanish. He attended San Juan de Letran College, and later transferred to the University of Santo Tomas to study law. He did not finish college and, at the age of 20, joined the secret society called Katipunan. He became the advisor on fiscal matters and secretary to Andrés Bonifacio. He was later known as Utak ng Katipunan. Jacinto also wrote for the Katipunan newspaper called Kalayaan. He wrote in the newspaper under the pen name Dimasilaw, and used the alias Pingkian in the Katipunan. Emilio Jacinto was the author of the Kartilya ng Katipunan as well.

After Bonifacio's death, Jacinto continued fighting the Spaniards. Like General Mariano Álvarez, he refused to join the forces of General Emilio Aguinaldo. He contracted malaria and died in Majayjay, Laguna, at the age of 24. His remains were later transferred to the Manila North Cemetery.