Ceramic from the Hellenistic, early and late Roman, Byzantine and the Middle Ages have been found here. In 1265, Baqa ash-Sharqiyya was among the estates Sultan Baibars handed to his followers, after he had defeated the Crusaders; the whole of Baqa ash-Sharqiyya was given to Emir'Ala' al-Din Aidakin al-Bunduqdar al-Salihi.
During early Ottoman rule, in 1596, Baqa ash-Sharqiyya was located in the nahiya of Qaqun in the Sanjak of Nablus. It had a population of 35 Muslim households, and paid taxes on wheat, barley, summer crops, olives, goats and/or bees, and a press for olives or grapes; a total of 14,000 akçe. In 1838 it was noted as a village, Bakah, in the western Esh-Sha'rawiyehadministrative region, north of Nablus. In 1882 the PEF's Survey of Western Palestine described Baqa as "a very small hamlet on high ground, with olives. It has a well to the south and a little Mukam to the north; scattered olives surround it, and there are two or three palms close by. A few houses stand separate, on the south east, near a second Mukam, called Abu Nar." A stone with Arabic inscriptions located over the entrance of the old village mosque could be the beginning of an endowment text. A population list from about 1887 showed that Baqa ash-Sharqiyya had about 180 inhabitants, all Muslim.
In the 1922 census of Palestine conducted by the British Mandate authorities, Baqa Sharkiyeh had a population of 269, all Muslims, increasing by the 1931 census to 330, still all Muslim, in 67 houses. In the 1945 statistics the population of Baqa ash-Sharqiyya consisted of 480, all Muslim, with a land area of 3,986 dunams, according to an official land and population survey. Of this, 173 dunams were designated for plantations and irrigable land, 2,870 for cereals, while 14 dunams were built-up areas.
Jordanian era
In the wake of the 1948 Arab–Israeli War, and after the 1949 Armistice Agreements, Baqa ash-Sharqiyya came under Jordanian rule. As part of the 1949 armistice agreements following the 1948 Arab-Israeli war, King Abdullah of Jordan ceded the captured Wadi Ara region to Israel in exchange for land near Hebron. This resulted in Baqa al-Gharbiyye falling on the western side of the Green Line, separated from its eastern counterpart, Baqa ash Sharqiyya. The separated towns still have close social and economic ties, however this has been reduced due to the completion of the West Bank barrier around the "Baqa enclave" of the Seam Zone. In 1961, the population was 952.
Baqa ash-Sharqiyya houses the Mother and Child Health Centre, which is used by the three surrounding Palestinian villages. The healthcare facilities for Baqa ash-Sharqiyya are designated as MOH level 3.
