It is believed that its name, Malolos came from Tagalog word “Paluslos” meaning downwards. The Spanish missionaries while searching for inhabited places came across some natives in a riverside barrio (now Canalate) and asked for the name of the place. Not knowing the Spanish tongue, these natives answered that the flow of the river in that part was downstream “Paluslos”, which was corrupted to Malolos by the Spaniards for euphony.
Malolos was founded in 1580 by the Augustinians under the direction of Fray Diego Ordoñez de Vivar.
As early as 1643, revolts were held against the Spanish government like the one initiated by Pedro Ladia.
The official separation did take place on August 31, 1859, dividing the town into three districts with respective capitanes municipales and parish priests. These towns were again reunited into a single municipality in 1903.
Prompted by Marcelo H. del Pilar, Jose Rizal (while in Europe on February 22, 1889) wrote to the 21 young women of Malolos praising them for their courage, initiative and nationalism when they longed for education as a tool against Spanish colonizers. Though promptly turned down by parish priest Fray Garcia, these women asked Gov. Gen. Valeriano Weyler to allow them to open a night school to be able to learn Spanish language.
The opening of Ferrocaril Manila- Dagupan Railways in April 1892 started the major development of the town.
Balangay Apuy, chapter or “balangay” of Katipunan in Bulacan province was organized in March 1896. Malolos Congress convened on September 15, 1898 at Barasoain Church. On the 18th, Aguinaldo proclaimed Malolos as the capital of the Philippines. The first important act of the Congress was the ratification on September 29, 1898 of the independence proclamation of June 12, 1898 at Kawit, Cavite. On October 19, 1898, by virtue of an act of Congress, the Universidad Literaria de Filipinas was established. It was in Malolos on December 20, 1898 when Gen. Emilio Aguinaldo declared December 30 of every year as a day of national mourning. The greatest achievement and for which the Malolos Congress was known was the framing of the Constitution, prepared by a committee headed by Felipe Calderon, was approved by the congress after amendments have been made on January 20, 1899, sanctioned by Aguinaldo the next day and promulgated on January 22. The last congressional act of the Malolos Congress was the inauguration of the Philippine Republic with Aguinaldo as the President on January 23, 1899, amidst the people’s jubilation. American forces captured Malolos on March 31, 1899.
By virtue of Public Law No. 88 of the Philippine Commission, Malolos became the capital of the province on February 27, 1901.
A plebiscite was conducted on December 18, 1999 for the ratification of the conversion of this municipality into a component city (Republic Act 8754). However, the conversion was rejected by the majority votes cast. As a result, a protest was filed impugning the results. Said protest was granted by the Second Division of COMELEC per Resolution No. EPC 99-2 which was promulgated on October 08, 2001 and became final and executory on November 08, 2001.