The municipality of Aglipay, Quirino was named in honor of the late Gregorio Aglipay, the head of the only existing religious sect in the community at that time. It was created through Executive Order No. 368 signed by the then President Elpidio Quirino on 11 November 1950 which reorganized the municipalities and municipal districts of the province of Nueva Vizcaya. It became one of the ten municipalities of the said province with an area of approximately forty one thousand one hundred twenty six (41,126) hectares. Its first seat of government was at Barangay Guinalbin with the late Hon. Gregorio Divina as its first appointed town Executive. It was then composed of only six barangays and inhabited mostly by Christians from the lowlands comprised mostly of Ilocano’s with some non-Christians tribes.

On 18 June 1969, Republic Act 4734 was enacted, creating Quirino as a sub province of Nueva Vizcaya, Aglipay, together with the municipalities of Diffun, Maddela, and Saguday, composed the new political unit.

This law was further amended through Republic Act 5554 enacted on June 21, 1969 which created the municipality of Cabarroguis and made it as the capital of the sub-province. The capital town’s creation resulted in the separation of three barrios and sitios from Diffun namely Gundaway, San Marcos and Mangandingay and thirteen from Aglipay, to wit, Zamora, Villamor, Burgos, Del Pilar, Eden, Bannuar, Mangandingay, Dibibi, Tucod, Dingasan, Bikbik, Malini and Capellangan.

With the creation of the province of Quirino through the Republic Act No. 6394 signed on 10 September 1971, Aglipay became one of the five municipalities of the province. The municipality of Nagtipunan was created later making the municipalities of the province into six.

The first elected Municipal Mayor of Aglipay was Hon. Flaviano Fontanilla who transferred the seat of government  from barangay Guinalbin to Barangay Pinaripad. However, when Hon. Gregorio Divina was again back in power as the elected mayor, he transferred the seat of governance to Barangay Progreso.

Aglipay is a third (3rd) class municipality and rank third (3rd) in land area of the province. The  municipal center is located at Barangay San Leonardo making the local government accessible to the town folks and the general public and at the same time promoting the growth of trade and commerce in the municipality.

It is now composed of 25 barangays namely: Alicia, Cabugao, Dagupan, Diodol, Dumabel, Dungo, Ligaya, Nagabgaban, Palacian, Pinaripad Norte, Pinaripad Sur, Progreso, San Benigno, San Leonardo, San Manuel, San Ramon, Victoria, Villa Pagaduan, Villa Santiago, Villa Ventura, Guinalbin, Ramos, Rang-ayan, San Antonio and San Francisco.

Assuming office last July 1, 2007 and reelected for a second term, Hon. Jerry T. Agsalda is currently the municipal mayor. He spearheaded may programs and projects, and his most-loved project is the transformation of the Municipal Hall into one of the landmarks of the province.