The municipality of General Emilio Aguinaldo used to be a separate Catholicparish in the town of adjacent Maragondon. It was founded by virtue of a decree issued on August 28, 1857 by Archbishop Fray Aranguren, OSA, of the Archdiocese of Manila. The decree separated the barrios of Batas and Guyong-guyong from the town of Maragondon, naming the new parish Bailen. It is recounted that a group of citizens from Barrio Batas petitioned Spanish Governor-GeneralFernando Norzagaray to convert their barrio into a municipality because of its distance from the town proper. Giving due course to the petition, the Spanish Governor approved the request on August 2, 1858.
Bailen, the town's original name, was coined from the Spanish word "bailar", meaning "to dance". Another claims that it was named after a Spanish town of the same name. The American civil government, from 1899–1901, reduced the number of towns to facilitate the military policy of concentrating the civilian population of the poblaciones. The Philippine Commission approved Act No. 947 on October 15, 1903, annexing the municipalities of Bailen and Mendez to Alfonso, thus becoming barrios of Alfonso. The Philippine Commission, for the second time in 1904, reorganized the entire province of Cavite reducing its 22 municipalities to 9 groups of towns. Bailen was annexed to Mendez. Bailen was reconverted into an independent municipality in 1915, with the complete restoration of peace and order in Cavite.
On June 19, 1965 with the signing of Republic Act no. 4346, the town's name, Bailen, was changed to General Emilio Aguinaldo, in honor of the first Philippine president who died the year before.
On September 3, 2012, the town's name was reverted to Bailen. The Sangguniang Panglalawigan (Provincial Board) has unanimously approved Committee Report 118-2012 renaming General Emilio Aguinaldo, a municipality in the 7th District of the province, to its original, "Bailen" during the 95th Regular Session. It is however, yet to be ratified.