[7] Clermont-Ganneau identified Ein Siniya with Biblical Jeshanah and Isana of Josephus, but modern authors place that at Kh.

[15] Claude Reignier Conder and Herbert Kitchener wrote in 1882 that a small Crusader fort appeared to have been situated there,[5] however, this has not been verified by later sources.

[15] Additionally, Conder and Kitchener mention the tomb with a Hebrew inscription that was discovered at the location, as well as a gateway adorned door that they thought was of Arab Christian origin.

[5][16] During Palestine's rule by the Ottoman Empire (16th-19th centuries), Ein Siniya was located in the sheikhdom of Bani Zeid, in the Jerusalem Sanjak.

The village had a population of 12 households, all Muslim, and paid taxes on wheat, barley, olives, vineyards, fruit trees, occasional revenues, beehives and/or goats; a total of 4,300 akçe.

"[5] Early in the 20th century, Ain Sinya was "practically" the property of a wealthy Arab native of Jerusalem who influenced authorities to build a carriage road next to Ein Siniya to benefit the village.

[4] At the same time it was noted that Ein Siniya, unlike other Arab villages in the area, grew mulberry and walnut trees in abundance instead of olive or fig groves.

[26] Moshe Sharett, later Prime Minister of Israel, lived in Ein Siniya for two years, in 1906-1908,[27] after the family's immigration from Ukraine.

The main cause of the growth of Ein Siniya, which was nearly empty after the 1967 war, was an influx of Palestinian refugees, who by 1997 constituted over half of the population (52.3%).