Diokno was born in Manila, the first of six children of Jose Manuel "Chel" Diokno, a lawyer and the founding dean of the De La Salle University (DLSU) College of Law, and Divina Aromin, a writer. He was named after his grandfather, the late Philippine senator and freedom fighter, Jose W. Diokno, the father of human rights and founder of the Free Legal Assistance Group (FLAG), who died six months before he was born. Pepe's great-grandfather is Gen. Ananías Diokno, leader of the Visayan forces during the 1896 Revolution and war against the United States.