The municipality of San Jose was formerly called "Ayuquitan", a name that was born due to a communication problem between the natives and Spanish Conquistadors.

The Spaniards approached the natives and asked the name of the place while pointing to the ground filled with piles of rice chaffs.

San Jose is the home of the old Spanish families settled since 1871 like the Patero, Amiscaray, Larena, Pareja, Siglos, Remollo, Renacia, Remata, Araco, Tatel and Remoto.

San Jose was created as a town in 1954 from the barrios of Ayuquitan, Basak, Basiao, Cambaloctot, Calo, Cancawas, Hanay-Hanay, Jilocon, Lalaan, Naiba, Tapon Norte, Tampi, and sitios Guinsayawan, Kang-atid, Kangdajonog, Guilongsoran and Kaputihanan of the barrio of Siapo, all of which formerly belonged to the former municipality of Ayuquitan and then part of the municipality of Amlan.

Niño, where a spinning sun is said to have manifested the visit of the Lady of Lourdes, devotees flock every Saturday of the month.