[3] According to a legend, the origin of town's present name San Rafael traces to a local fisherman.

[5] The San Juan de Dios Church still stands as the silent witness of the bloody battles that the Filipino insurgents fought during the Philippine Revolution of 1896.

This church was used as military barracks for almost three days, after the insurgents had destroyed all papers and documents they found in the convents.

Since then, with the supervision of the American administrators, San Rafael has enjoyed the education and the progress which was denied to them during the three–century rule of the Spaniards.

The people of San Rafael evacuated to Upig, Licheria, Coral na Bato and Camachile.

Uncaptured Filipino army units, a communist insurgency and supporting American agents all played a role in the resistance.

However, the unity of the people of San Rafael and the heroism of the Filipino soldiers and guerrillas prevented further casualties and destruction.

Local Filipino troops of the 32nd, 35th and 36th Infantry Division of the Philippine Commonwealth Army and 3rd Constabulary Regiment of the Philippine Constabulary liberated the town in San Rafael, Bulacan and aided the guerrillas of the Bulacan Military Area (BMA) and defeated Japanese soldiers and aftermath in World War II.

[11] On December 14, 2024, the municipality set a Guinness World Record for the "largest gathering of people dressed as angels," which was held by Winnipeg, Canada, in 2015.

Poverty incidence of San Rafael Source: Philippine Statistics Authority[19][20][21][22][23][24][25][26] In April 2023, the San Rafael Heights Township Development Project, a socialized housing innovation, based on Pambansang Pabahay Para sa Pilipino (4PH) started the construction of 3,920 residential condominium units in a seven-hectare lot in Sitio Gulod, Barangay Caingin.

Its amenities include a clubhouse, basketball court, park and playground, garden walkway and jogging path.

The historical marker was unveiled on 17 August 2022 by Carminda R. Arevalo, OIC, NHCP and San Rafael Mayor Mark Cholo Violago with G. Leween V. Castro and G. Alvin R. Alid.

Barangay Caingin Resolution of June 24, 2022 declared it "Bahay na Malaki" as Heritage House by Captain Ramilito B. Capistrano and all Councilors.

Built in 1890, this 19th-century architecture in the Philippines with its Azotea built in 1957, is owned by Vicente Trinidad dela Fuente (November 14, 1866 – December 16, 1920) a Cabeza de Barangay or Kapitan, husband of Paz Lim Villaroman (February 18, 1875 – March 20, 1913) with children Amanda (February 20, 1891 – January 14, 1960), Luisa, Luisa, Araceli (November 25, 1895 – April 7, 1995) and Dolores-Lolita (December 31, 1898 – April 18, 1986), all spinsters, who established the "dela Fuente Lines".

Their cousins Leticia Trinidad Gonzales and Dalisay Lim Cruz, teacher, built the Caingin chapel.

On December 14, Senator Imee Marcos witnessed the civic engagement of 2,000 residents dressed in white robes, halos, and wings at the Victory Coliseum, Town Hall.

More than a thousand children in angel costumes in the street make it look like heaven has come down to the town of San Rafael.