Years ago, Binalbagan was called Inabagan, “the haven of refuge”. Negritoes inhabited this settlement until the arrival of the Mundos. Between 100 and 1300 A.D. Malays belonging to the 10 Bornean datus and their families settled in Binalbagan. During the Pre-Spanish era, three groups of people namely; the Mangyans, the Pintados and the Agtas inhabited the place. 

In 1571, the Spaniards came and established in Binalbagan the largest encomienda in the island. Binalbagan, along with the Municipality of Oton, both established in 1572, are the two oldest towns in Western Visayas. As such it had earned the title, Banwang Panganay. 

Two stories are told on the origin of the name Binalbagan. During stormy nights, the cargo of shrimps get wet and are partially spoiled. To remove the slimy odor and preserve the shrimps, the traders would beat the barks of mangroves to extract juice believed to contain preservatives for the shrimps. The action of beating the bark was termed as balbag in the native dialect. Hence, the place where the beating was done was called Binalbagan. 

Old folks however, say that the town got its name from a past incident when a very big snake was stranded in the mouth of Binalbagan River, blockading sea transport. People referred to the place and incidents as Binalbagan. Subsequently, the name evolved into Binalbagan. Binalbagan today is known for its home-made candies (sweets) probably because of the presence of the Binalbagan-Isabela Sugar Company (BISCOM).