Isa Khan was born on 17 April 1536 into a zamindar family known as the Dewans of Sarail in the Bhati region of the Sultanate of Bengal.

His father Sulaiman Khan, originally named Kalidas Gajdani, converted to Islam and carved out a principality in Bhati.

[4][5] Abu'l Fazl, in his Ain-i-Akbari, calls him "Isa Afghan", though in the Akbarnama assigns the Bais Rajput origin.

[8] Following the death of Sultan Mahmud Shah, Isa's father declared himself as the legal successor and revolted against the Sur Empire.

He gradually increased his power in the Bhati region by making alliance with other Zamindars and helping fellow Afghan Chieftains.

[13][14] In 1577, Isa established Egarasindhur (in present-day Pakundia Upazila, Kishoreganj) as the political and trading centre of his realm.

[1] Isa faced the Mughal force led by Shah Bardi and Muhammad Quli on the Sarail-Juan Shahi border in Kastul on the bank of Meghna river.

With the good grace of the queen Amrabati, the king granted an army of 52,000 men to help Isa face the Mughals.

[21] In September 1584,[22] the then-subahdar Shahbaz crossed the Ganges near Khizirpur and attacked Sonargaon, Katrabo and Egarasindhur[1] and pursued the defeated Pathan forces under Masum Kabuli up to Bikrampur in Dhaka, the cunning Isa then pretended to negotiate for surrender and delayed the attack of the Mughal general for several months.

He even promised the Mughals he would dispatch Ma'sum Khan Kabuli, the renegade to a compulsory Pilgrimage to Mecca, something that was viewed as an act of banishment.

In late 1586, Ralph Fitch, an English traveler and merchant, came to Sonargaon, Bengal's eastern districts and stated, They be all hereabout Rebels against the King Zebaldin Echebar (Jalaluddin Akbar) for here are so many Rivers and Iands, that they flee from one to another, whereby his Horsemen cannot prevaile against them.

[29] Isa was emboldened to resist the Mughals after he successfully sought alliance with Raghudev, his former enemy[30] and Kedar Rai, Zamindar of Bhusna in Faridpur.

[31] In the clash that took place in August 1597, Isa became engaged in a battle against Mughal naval forces with the assistance of Masum Khan Kabuli, an ex-Mughal defector.

[33] However, the duel ended inconclusively when Isa Khan stopped fighting after Man Singh's sword broke.

[citation needed] Due to his submission, Akbar assigned 22 parganas or administrative units under the ruling of Isa.

[34] Khan first married his maternal cousin Fatima Bibi, a daughter of his aunt Raushan Akhtar Banu and her husband Syed Ibrahim Danishmand.

[39] Monwar, leading naval ships armed with bronze 9,5 inches cannons, recovered Chittagong from the Portuguese.

[39] Haybat Khan, another grandson of Musa, established Haybatnagar (in present-day Kishoreganj district) and made it the centre of his land-lordship of seven parganas.

[26] James Wise (d. 1886[41]), a civil surgeon in Dhaka for 10 years, published a report on Baro-Bhuyans in Journal of the Asiatic Society of Bengal, Volume 43 in 1874.

[42] As of 2005, Dewan Amin Dau Khan, the 14th descendant of Isa has been living in Jangalbari Fort in Egarasindur village.

Rattled by this, Kedar Ray invaded Isha khan's capital, tearing down the Kalagachhia and other forts one after another up until his death in 1599.