History of Baksa district was identified as a district of Bodoland Territorial Council in October, 2003. From 1st June, 2004 onwards, the district of Baksa started functioning officially. The Baksa district was a portion of the districts of Kamrup, Barpeta, Darrang and Nalbari.

On 10th February, 2003 the Bodoland Territorial Autonomous District (BTAD) was signed as per the guidelines of the Bodoland Territorial Council or BTC. Three other districts of Udalgiri, Chirang, Kokrajhar were also a part of this category. A major portion of the local population chooses to address their district as "Bagsa", rather than Baksa. Scholars are of the view that the term "Bagsa" is actually a derivation from the word "Bangsa" which is a "Dzonkha" word. This Dzonkha word implies a corridor, along with a farmhouse. It is said that the king of Bhutan and his subjects utilized this region for the purpose of conducting trade activities.

However, there are other opinions which have asserted that the word "Bagsa" has been traced from the Bhutanese language. This area was previously referred to as "Bagsa Duar". Bagsa refers to a type of rice and Duar means the point of entry. Since the king of Bhutan had reigned these portions of the country for a considerable amount of time around the 19th century, it is believed that the name Bagsa might have originated from there. Bodo sources state that this name was born from a type of rice grain, which is termed as "Bagsa". This rice grain is broken.

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