The history of Gonzaga can be traced back from the 17th century. Its aborigines were the Negritoes who lived and survived through wild fruits and crops in the forest. Hunting and fishing supplemented their source of living .Its original name was GAMPAO, named by native inhabitants, which meant mountainous.

Later it was called WANGAG because of its abundant clear rivers and creeks. Then came the adventurous and civilized Ilocanos who hailed from the Ilocos Region. Their settlement into the place caused the negritoes to fled to the jungle. They were treated as minorities by the Ilocanos, which caused a feud between the two and lasted for so long and until the reign in this area of Spanish missionaries.

Gonzaga stated its political identity as a Barrio of Buguey. It was given ecclesiastical recognition on February 23, 1898 with Nuestra Senora del Pilar as its Patroness.
In 1917, due to the advent of physical, social and economical progress, WANGAG was renamed RUMANG-AY , meaning to be progressive. In the same year, a noted pioneer leader. FRANCISCO TORRES initiated and submitted a petition converting the place into an independent town. With this, then Governor General Frank Burton Harrison signed and issued Executive Order No. 81 on November 7, 1917 creating the municipality of GONZAGA with its effectivity on January 1, 1918. The municipality was named in honor of GRACIO GONZAGA, the first Filipino Provincial Governor of Cagayan.