The present day Pudtol is the remnant of the Old Municipal District of Tawit, which existed since August 13, 1908. The Municipal District of Tawit comprised the territories of the present day municipalities of Luna, Flora, Sta. Marcela and Pudtol, and some part of Allacapan and Lasam in the province of Cagayan. The seat of government then was at Barrio Tawit (the present Barangays of Malibang, Matanguisi, Aga and Cacalaggan).
On December 3, 1929, the Municipal District of Pudtol was created by virtue of Executive Order No. 217 signed by President Ramon Magsaysay, inheriting all territories left of the old Municipal District of Tawit after the organization of the Municipal District of Luna.
In February 1957, the first set of appointed municipal officials of Pudtol were inducted into office. Emilia Almasan was the municipal mayor. On March 31, 1959, President Carlos Garcia signed Executive Order No. 335 converting the municipal district of Pudtol into a regular municipality making it the first municipality in Kalinga and Apayao to attain such status. On June 22, 1963, the municipality of Flora was created by virtue of Republic Act 3672 to comprise the eastern barangays of Pudtol, thereby reducing Pudtol to its present size.
From 1960 to 1963, Juan Madriaga was elected as the mayor, followed by Antonio Jadsac who was appointed from 1963 to 1980. Domingo Agngarayngay was appointed from 1980 to 1986, succeeded by Robert Bangay, who was appointed from August, 1986 to November 30, 1987; then from December 6, 1987 to February 1, 1988, Russel Caluducan was appointed as mayor. Batara Laoat won in the 1988 and 1992 elections. In 1998, Johnny Ilayat was elected as mayor.