He was born on May 26, 1859 to Ramon Agoncillo and Gregoria Encarnacion. Even at an early age, his parents already noted his extraordinary intelligence. He enrolled at the Ateneo Municipal where he was a consistent honor student. He later transferred to the University of Santo Tomas and obtained his Bachelor of Arts with an excellent grade. He was granted a Licentiate in Jurisprudence with the highest honors. After a year of law practice in Manila, he returned to Taal to administer his family’s properties as both his parents had died.

In Taal, he rendered free legal services to the poor and oppressed. His activities raised the ire of the parish priest and some residents who accused him of being anti patriotic, anti religious and denounced him as a filibustero. His deportation was recommended but he was forwarned. He briefly fled to Japan and transferred to Hongkong where he joined other Filipinos in exile. After the signing of the Pact of Biak-na-Bato, he headed the Central Revolutionary Committee as procurement office and propaganda agency of the Revolutionary Government. When hostilities broke out between Filipinos and Americans, the Philippine Revolutionary Government commissioned Agoncillo as Minister Plenipotentiary to conclude treaties with foreign governments. He and Sixto Lopez went to Washington DC but US President McKinley did not receive them. To drum up sympathy to the Philippine cause, they addressed the American Episcopalian bishops.

Agoncillo proceeded to Paris, France to present the Philippine cause at the peace conference convened between Spain and the US but he was ignored. Two days after the signing of the treaty, he presented a formal protest to the president and delegates of the Spanish-American Commission saying that Spain had no legal right or status with respect to the Philippines since the Spanish government was no longer in authority over the country and that the only authority existing was that of the Filipinos themselves. Agoncillo tried his best to block the ratification of the Peace treaty – to no avail.

On July 15, 1901, Agoncillo returned to Hongkong and rejoined the Junta and later returned to the Philippines after the Filipino American hostilities. In 1907 he represented Batangas in the Philippine Assembly. His legal brilliance shone in his defense of El Renacimiento whose editors were charged with libel by Dean C. Worcester. In 1923 during the administrtion of Governor General Leonard wood, he was appointed Secretary of Interior.

He died on September 29, 1941