Al-Batani al-Sharqi, like the rest of Palestine, was incorporated into the Ottoman Empire in 1517, and in the tax registers of 1596, it was a village in the nahiya of Gaza, east of Isdud, north of Bayt Daras and part of the Sanjak of Gaza with a population of 39. Al-Batani paid taxes on wheat, barley, fruit, beehives, goats, and vineyards. The whole population was Muslim. The village appeared as an unnamed village on the map of Pierre Jacotin compiled in 1799. In 1838, Robinson noted el-Butaniyeh, the east, as Muslim village located in the Gaza district. In 1863 the French explorerVictor Guérin visited the village which he called Bathanieh Ech-Charkieh. He found about one hundredadobe brick houses, and ancient stones laying on the ground nea a well. Tobacco plantations grew in gardens surrounded by cactus hedges. Socin, citing an official Ottoman village list compiled around 1870, noted that Al-Batani al-Sharqi had 89 houses and a population of 265, though the population count included men, only. Hartmann found that el-batanije esch-scharkije had 85 houses. In 1882, the PEF's Survey of Western Palestine described al-Batani al-Sharqi as being situated on low ground and extended from east to west in a rectangular shape. Patches of garden and a number of wells surrounded the village.
In the 1922 census of Palestine, conducted by the British Mandate authorities, Batani Sharqi had a population of 304 inhabitants, all Muslims, increasing in the 1931 census to 404, still all Muslim, in 85 houses. Construction expanded westward—the Wadi al-Mari's winter flooding impeded eastward expansion—along the road that linked to al-Batani al-Gharbi until the distance between the two villages was less than. Village houses, made of adobe, with wood-and-cane roofs, were built close together along narrow alleys. The two al-Batanis shared an elementary school that was opened in 1947; its initial enrollment was 119 students. The village had a mosque and a number of small shops. The entire population was Muslim. In the 1945 statistics Al-Batani al-Sharqi had a population of 650, all Muslims, with 5,764 dunams of land, according to an official land and population survey. Of this, 319 dunams were allocated to citrus and banana plants, 474 plantations and irrigable land, 4,733 used for cereals, while 32 dunams were built-up land.
In early May, 1948, the Al-Majdal Arab National Committee,, ordered the villagers of Al-Batani al-Sharqi, together with those of Al-Batani al-Gharbi, Yasur, Bayt Daras and the three Sawafir villages to stay put. It became depopulated shortly afterwards as part of Palmach's 'Operation Lightning'. After they had hit Bayt Daras, the operational orders to Haganah on the 10 May was to "subdue" Al-Batani al-Gharbi and Al-Batani al-Sharqi, "with the same means used vis-à-vis Aqir, Bashshit and Bayt Daras." Together with nearby Bashshit and Barqa, al-Batani al-Sharqi was captured by the Haganah's Givati Brigade, just before the end of the British Mandate period in Palestine. According to Israeli historian Benny Morris, it fell on May 13, 1948, as part of Operation Barak in which the Haganah moved southwards in anticipation of an engagement with Egyptian forces. The History of the War of Independence, however, states that it was captured by Israeli Jewish forces under the Givati Brigade's Eighth Battalion on June 10–11. Palestinian historian Walid Khalidi said that this may have meant that the village briefly changed hands in the course of Israeli-Egyptian battles on the southern front before the first truce came into effect on June 11. Following the war the area was incorporated into the State of Israel, with the villages lands remaining undeveloped. In 1992 the village site was described: "Only a dilapidated police station from the Mandate period survives. It is a complex of three single-storey, concrete flat-roofed buildings. One of the buildings is higher than the other two; all three have rectangular doors and windows. A village street is clearly visible. Cactuses and fig, eucalyptus, and sycamore trees are scattered over the site. Israeli farmers cultivate citrus on the adjacent lands."
