The area near the church and shrine received the name "Pinaglabanan" (Tagalog for "battleground") as the Katipunan engaged the Spanish Empire in the Battle of San Juan del Monte, marking the start of the 1896 Philippine Revolution.

Although the parish was established on July 15, 1894, the construction of the first church happened a year after, under the supervision of architect Luis Arellano and the financial support of Mariano Artiaga.

[4] On August 30, 1896, the Battle of San Juan del Monte between Filipino and Spanish troops occurred on the tract of land fronting the newly built church.

[3] The St. John the Baptist Church was declared as a historical landmark through San Juan Municipal Council Resolution, Ordinance No.

[3] On May 15, 1994, the Feast of the Ascension, Cardinal Jaime Sin, Archbishop of Manila, blessed and inaugurated the new San Juan Centennial Belfry, built to commemorate the church's hundredth anniversary.

Architects Renato Berroya and Arsenio Topacio designed the structure, which matches the façade,[5] and houses the church bell that dates to 1896.