During the War of the Pacific, a division of Orozimbo Barbosa marched through the area, then part of Ate District, at 7 a.m. on January 9, 1881, with the intent to deceive local Peruvian troops under the command of Mariano Vargas and divert them to the area to defend the city against an east-to-west attack instead of a southern advance, which actually took place.[2][3] Both armies clashed at what became known as the Battle of La Rinconada de Ate, with the Peruvians being defeated and the eastern entrance to the city left wide open, although such an entrance was ultimately not used.[4]
The area began to be urbanised during the 1950s.[1][5] On February 6, 1962, La Molina was established as a district separate from Ate.[1] The mining area of La Planicie de Pampa Grande was included in the district through its prior acquisition by the Aparicio-Figari Group, contributing about 50% of its territory, from which the neighbourhoods of La Planicie, El Lago and Las Lagunas were created.[2] A number of artificial water bodies were created with water from Rímac River taken to the new neighbourhoods,[6][7] with more developments taking place on the western side of the area.[8]
In 2023, 49 Malaysians—23 men and 26 women—were released from their illegal custody in a house next to Villa María School after a raid by police, with 6 Taiwanese and 2 Peruvians, who acted as the residence's security guards, arrested.[10][11][12]
In 2024, a mass grave with the remains of at least three people was discovered near the neighbourhood's eastern limit with Cieneguilla.[13][14]