Be'er Ya'akov was established in 1907 on 2,000 dunams of land purchased by a company headed by Meir Dizengoff from a Lutheran German colony the previous year. It was divided into two sectors, one for immigrants from Russia, Poland, Romania, Bulgaria, Argentina, and Iran, and the other for Mountain Jews from Dagestan. It was named after Ya'akov Yitzhaki, a rabbi and pioneer from the Mountain Jewish community. Yitzhaki headed the Mountain Jewish pioneers who settled there.
In 1909, there were 25 families living in Be'er Ya'akov, and tensions between the Ashkenazi and Dagestani families. In 1910, the first elementary school was established. According to a census conducted in 1922 by the British Mandate authorities, Be'er Ya'akov had 131 inhabitants, which had increased in the 1931 census to 265 residents in 58 houses. By 1947, it had a population of 400. It achieved local council status in 1949.
During the 1948 Arab–Israeli War, and until the Israeli capture of Ramla in July 1948, Be'er Ya'akov was on the front line. The population at that time was evacuated and a new settlement, Be'er Shalom, was established nearby by members of Kibbutz Buchenwald, the first pioneer training group formed in post-World War II Germany.
The town is growing rapidly, with massive urban development, including the construction of new neighborhoods taking place, and it is expected to gain city status in the coming years. In 2017, a new plan was approved to massively expand Be'er Ya'akov in area and population. Once the Tzrifin complex of military bases is vacated and most of the bases are relocated to the Negev, Be'er Ya'akov will expand onto land once occupied by military facilities. It is planned that Be'er Ya'akov will eventually have a population of 100,000.