Agoncillo wrote abundant books and papers about Philippine History. To name a number of his famous works are History of the Filipino People; The Crisis of the Republic; The Revolt of the Masses; The Story of Bonifacio and the Katipunan; Ang Kasaysayan ng Pilipinas; and the Malolos, Philippine History (adopted as official textbook in Philippine History).
Agoncillo was known as the drastic historian that became a National Scientist. He was also given the highest appointment title in all universities, the University Professor.