The village of Batnaya was first attested in the 7th century, around when it is believed to be converted to Christianity by Mar Oraha, a comptemporary of the Church of the East.
In 1235, the Mongols invaded, causing destruction as they passed through the area.
In the early 1700s, the village was converted to Chaldean Catholicism. In 1743, Persian Emperor Nadir Chah attacked, pillaged, and ruined the entire region, including Batnaya.
Several outbreaks of the plague occurred in the Nineveh plain in 1737, 1773, and 1828.
The population of the village continued to grow up until 2014, having a population of around 6000 people.
All of the inhabitants of Batnaya were forced to leave the village on the night of the 6th of August, 2014 to escape from ISIS forces. The village was ransacked and vandalized by ISIS, with the church and other religious sites being the most targeted for destruction.
The village was used a frontline by ISIS while they shelled Kurdish troops during the war. It was one of the worst hit areas, destroyed first by the ISIS invasion and then by a coalition airstrike. By the end of the occupation, the village's churches were destroyed and ransacked, and only 1% of the village's 997 houses remained intact - it was the most destroyed town in the Nineveh Plains.
The village was taken back from ISIS on the 20th of October, 2016. The Peshmerga (Kurdish Security Forces), in cooperation with Canadian, French, and American teams, cleared the village of mines and bombs.
Reconstruction of Batnaya was delayed by ISIS-planted booby traps and tunnel systems underneath the village, as well as disputes between the Iraqi Government and the Kurdistan Region.
Since it was liberated, over 400 houses have been rebuilt by the United Nations Development Programme.
The first 10 families return to Batnaya in Summer 2019. Since then, people have continued to return to the village as more of it is rebuilt and the region stabilizes.