The name of the municipality was derived from its patron saint “Sto. Niño”, means the Holy Child. It was formerly Barrio 13 of Norala Settlement District of the defunct National Land Settlement Administration (NLSA), which was founded in 1947.
In 1980, the Sangguniang Panlalawigan of South Cotabato passed a resolution requesting Assemblyman Jose T. Sison to sponsor a bill creating Sto. Niño into a municipality. This resolution merited action and Parliamentary Bill No. 1220 was passed and approved last December 18, 1980, signing it into law as Batas Pambansa Bilang 90. The people in a plebiscite held last April 7, 1981, overwhelmingly ratified the law.
The town territory is a detachment of barangays from the mother municipality, Norala and from the Municipality of Banga, South Cotabato and Bagumbayan, Sultan Kudarat. It has a total land area of 10,973 hectares comprising of 10 barangays.