Regional Bobota Canal, the first major water management project in modern-day Croatia in the post-Roman Empire period, was named after the village.

According to the story, the ancestors of today's inhabitants of villages, who settled at the time of the Great Serb Migrations under Arsenije III Čarnojević, were called Bobe.

The earliest recorded human settlement in the area of Bobota dates back to classical antiquity with the northeast archeologically site of Staro Ljeskovo containing IV century Roman bricks marked with "I H" inscription.

[8] Other types of artefacts were discovered at the same location including Roman glazed ceramics, terra sigillata, glass and oil lamps with reliefs and a stone altar with the inscription of the tribune "Titus Flavius Marcianus" and with recognized potential for further archaeological excavations.

In following years Serb settlement continued with families arriving from Bačka, Mačva, Montenegro and Baranya so that in 1736 there was already 82 households.

[12] From 27 December 1920 (when they arrived in Vukovar) soldiers and families of the White Russian émigrés who were followers of Pyotr Wrangel settled in Bobota, Pačetin, Trpinja and Vera.

[17] Thirty of them were sent to the Jadovno concentration camp, while 15 were sentenced to death by a hastily convened traveling summary court and execution being carried at the Dudik site.

[17] 96 residents of Bobota lost they lives during the World War II resulting in post-war reputation of the village as a regional stronghold of the resistance movement.

Rural resistance to this policy led to an incident in Bobota in 1945 when an anonymous humorous graffiti appeared in the village subsequently described by new authorities as an "enemy act by kulak elements".

[19] After the local branch of the Communist Party collectively joined the SDS, in October of 1990 300th anniversary of the Great Migrations of the Serbs was marked in the village with Matija Bećković attending the event.

[23] Kindergarten is named after fictional island nation of Lilliput from the Gulliver's Travels book written by the Anglo-Irish writer and clergyman Jonathan Swift.

Since the institution operate in villages where Serbs of Croatia constitute majority, it offers its program in Serbian with additional mandatory learning of Croatian.

[24] The school building has 8 classrooms, 7 specialized cabinets, two offices, library, staff room, toilets and central heating.