Mapúa was born to Juan Mapúa and Justina Bautista de Mapúa on December 21, 1888 in Manila. His education started at the Ateneo de Manila University and at the Liceo de Manila. In 1903, he was sent to the United States to complete his high school education and college education as one of the "pensionado" students of the United States. The 1903 Pensionado Law awarded university scholarships to the US for Filipino exemplary Filipino students. In exchange, they agreed to work on local government construction projects. He completed his secondary education at the Boone’s Preparatory School in Berkeley, California and obtained a degree in architecture at Cornell University in Ithaca, New York.