Mazkeret Batya was established on November 7, 1883 by 10 pioneers from Russia and 7 local Jews. It was originally called Ekron, the first agricultural settlement of the Hovevei Zion movement. The land was purchased by Baron Rothschild in an early attempt to introduce Jewish farming in Palestine. Rabbi Shmuel Mohilever was instrumental in mobilizing funding and organizing the settlers. Mohilever's remains were later reinterred in the Mazkeret Batya cemetery. In 1887 the name was changed to Mazkeret Batya, in memory of Betty Solomon de Rothschild, mother of Baron Edmond James de Rothschild
The economy of the village was originally based on dry farming, which continued even after the Mekorot Company constructed a pipeline to bring water from Rehovoth. In 1947, Mazkeret Batya was home to 475 people.
During the Mandate era, a Jewish police station was established in Mazkeret Batya to safeguard the local roads. In the War of Independence, convoys to besieged Jerusalem left from Mazkeret Batya. A field hospital operated there to care for Haganah fighters wounded at Latrun.
According to one source, at the end of the British Mandate for Palestine, the British tried to hand the nearby Aqir airfield and camp to the Palestinian Arabs, apparently without
