The Greater Noakhali district region predominantly includes the districts of Noakhali, Feni and Lakshmipur, although historically included the island of Sandwip in Bay of Bengal. The history of the undivided Noakhali district region begins with the existence of civilisation in the villages of Shilua and Bhulua. Bhulua became a focal point of Bengal during the Buddhist and Hindu kingdoms of Pundra, Harikela and Samatata leading it to become the initial name of the region as a whole. The medieval Kingdom of Bhulua enjoyed autonomy under the Bengal Sultanate before being conquered by the Mughal Empire. At the beginning of the 17th century, Portuguese pirates led by Sebastian Gonzales took control of the ara but were later defeated by Governor Shaista Khan. Affected by floodwaters, the capital of the region was swiftly moved to a new place known as Noakhali, from which the region presently takes its name. By 1756, the British East India Company had dominated and started to establish several factories in the region. The headquarters was once again moved in 1951, to Maijdee, as a result of Noakhali town vanishing due to fluvial erosion.

Ancient and early medieval Civilisation in the present-day Noakhali region dates back around 3000 years ago, making it one of the youngest sub-regions of Bengal. It was under the realm of Samatata division in south-eastern Bengal. According to Hindu mythology, this region may have been a part of the Shukhma Kingdom. The Hindu epic known as the Mahabharata states that the King of Shukhma was defeated by Bhima, who enforced tribute and seized the gems belonging to the kings of this region. The Allahabad Pillar states that Samatata came under the influence of Samudragupta in the 4th century. The 5th-century Classical Sanskrit author Kalidasa mentions the greenery and palm trees of Shukhma in his Raghuvaṃśa. An undeciphered Brahmi inscription dating back to the Mauryan and Shunga period was discovered in the village of Shilua. The discovery of silver proto-Bengali coins suggest that by the 9th century, the region was a part of the realms of Harikela and Akara. The region was historically known as and based around Bhulua, an ancient town a few miles west of the town of Noakhali. Bhulua was a part of the Pundra Kingdom for much of this period and later under the Khadgas, Harikelans, Chandras, Varmans, Senas and Devas.

The early Rajas of the region were said to have been Kayasthas from West Bengal. According to Hindu legend, Adi Sura's ninth son, Bishwambhar Sur, went on a pilgrimage to the Chandranath Temple atop the Chandranath Hill of Sitakunda. Returning from Sitakunda, Sur passed through present-day Noakhali where he rested and had a dream that Varahi would make him the sovereign of this territory if he worships her. On a cloudy day in 1203 AD, Sur built an altar for Varahi and sacrificed a goat. When the clouds moved away, Sur realised that he had sacrificed the goat to the west, which was not acceptable in Hinduism. As a result, he screamed bhul hua (it was wrong), from which the name Bhulua was said to have come from. Today, the Hindus of Noakhali continue this local tradition by sacrificing goats to the west. Though ancestrally a Rajput, Sur married into a Kayastha family, which his dynasty continued to identify with. A temple in Amishapara, Sonaimuri still contains a stone idol of Varahi. According to tradition, Kalyanpur became the first capital of the Bhulua Kingdom.

In this period, the native Bengalis of the region were said to have been spirit worshippers as opposed to the Benaglis of western and northern Bengal at the time. Prior to this, Hinduism and Buddhism was prevalent in the region.

Arrival of Muslims

Islam was said to have first reached the region under the Delhi Sultanate, when Governor Tughral Tughan Khan militarily assisted the nearby Twipra Kingdom in 1279. The armour-bearer of Bahram Khan, the Governor of Sonargaon, was Fakhruddin Mubarak who was said to have his office in Noakhali initially. Some historians have even claimed that Mubarak was born in eastern Noakhali, near Chaprashirhat. The Sharshadi Shahi Mosque in Feni is attributed to Mubarak. After the death of Bahram Khan, Mubarak moved to Sonargaon where he ruled as an independent Sultan. His reign marked the construction of a road from Chittagong to Chandpur via Noakhali. The nearby Sultan of Satgaon, Shamsuddin Ilyas Shah, may have also passed by Noakhali during his raid of Tripura.

The Hindu kingdom of Bhulua remained in the hands of the Bishwambhar Sur (বিশ্বম্ভর শূর) dynasty. The fourth king of Bhulua adopted the name Sriram Khan which suggests that Muslim influence began around this time. Khan founded the village of Srirampur where he built a palace which still exists in ruins today. The sixth king ended the tradition of naming themselves as Khans and adopted the title of Rai. His son however, adopted the name Manikya which suggests that Bhulua may have become a vassal state of the Manikya dynasty's Twipra Kingdom. They had cordial relationships, with the Maharajas of Tripura allowing the Bhulua kings to place the Raj Tika (royal mark) on their foreheads during their coronation.

To strengthen the defences of the Bhulua Kingdom's frontier from the invasion of the Maghs, Bhulua's king Rajballabh appointed a Muslim general to be a feudal governor of the Elahabad and Dandra parganas. This led to an influx of Muslim migrants into the region. In this period, a Sufi pir and Syed from Baghdad arrived to Bhulua riding on top of a tiger and was thus known by the people as Sher Alam. The Hindu ruler gifted to Syed Sher Alam, two droṇs of land and a large rent-free house in Danaikot, Feni. Alam stayed in Danaikot for a while before setting off to join the Muslims who had settled in Dililpur/Tangirpar (near Rajganj), where he was accepted as their chief. Alam became the founder of the aristocratic Syed Alam family of Rajganj who played important roles in the political history of Noakhali. Syed Nur Alam Chowdhury was from this family.

In the 14th century, Syed Ahmad Tannuri of Baghdad migrated to Kanchanpur, with the intention of propagating Islam. He is also known by locals as Miran Shah. He was accompanied by his wife, Majjuba Bibi, and some companions such as Bakhtiyar Maisuri who settled in Rohini, Shah Muhammad Yusuf in Kitabpur, Shah Muhammad Fazalullah in Raipur, Shah Nuruddin in Bhatuiya, Shah Badshah Mian in Dalilpur Tangir Par, Miyan Sahib Baghdadi in Harichar, and Shah Abdullah and Shah Yaqub Nuri in Noakhali town. Following the Conquest of Sylhet in 1303, some disciples of Shah Jalal migrated to Noakhali, such as Shaykh Jalaluddin who settled in Nandanpur. Other notable Muslim preachers who settled in Noakhali include Ahsan Hasan Shah, Azam Shah and Shah Amiruddin.

Lakshmana Manikya was the eighth and most prominent king of Bhulua. He authored two Sanskrit dramas, Bikhyata Bijaya and Kubalayasva Charita, and was a member of the 16th-century Baro-Bhuiyans of Bengal. Hundreds of Brahmins were invited to Bhulua by Manikya, who gave them land in Chapali, Kilpara, Barahinagar and Srirampur. His court scholar Pandit Raghunath authored Kautuka Ratnakara. Manikya would often make fun of Ramchandra, the young ruler of Bakla and Chandradwip, which eventually led to Ramchandra plotting against him. Ramchandra crossed the Meghna River and invited him to a banquet in which his men captured Manikya and murdered him back in Chandradwip.

Lakshmana was succeeded by his son, the ninth King of Bhulua, Durlabha Narayan Balaram Manikya. Balaram Manikya's court poet was Abdur Razzaq of Balukia in Bedrabad, who wrote Sayful Mulk o Lal Banu in 1770 CE. Unlike the former kings of Bhulua, Balaram refused to attend the coronation of the Twipra Raja Amar Manikya, as he perceived him to be an illegitimate ruler and essentially declared total independence from Tripura. Some sources claim this was in 1579, while others in 1578. As a result, Amar Manikya raided Bhulua and Balaram was eventually forced to become a vassal ruler again. Amar Manikya was digging a tank, now known as Amar Sagar, in his capital at Udaipur for religious reasons and demanded various chieftains to supply labour for this task and pay tribute. The Rajmala chronicles highlights Bhulua sending 1000 labourers for the task.

Mughal period

In the late 1580s, King Min Phalaung of Arakan invaded much of present-day Noakhali. The Mughal invasions and conquests in Bengal started during the reigns of Emperors Humayun and Akbar. Present-day Noakhali was a part of the Sarkar of Sonargaon and divided into three parganas: Bhalwa Jawar (Bhulua), Jogidia (Jugdia) and Dandra. The pargana of Bhalwa Jawar encompassed several former parganas such as Amirabad, Tappe Aswadia, Babupur, Chakla Ghoshbag, Gopalpur, Jainagar, Mirzanagar and Ramchandrapur.. The Battle of Rajmahal in 1576 led to the execution of Daud Khan Karrani, ending the Karrani sultanate. Bengal was fully integrated as a Mughal province known as the Bengal Subah by 1612 during the reign of Jahangir. Amirabad was established as the fourth Mughal pargana of Bhalwa, situated in the centre. The Mughals briefly captured Sarkar Udaipur which is how Chhagalnaiya became a part of greater Noakhali.

During the reign of Mughal emperor Jahangir, the Subahdar of Bengal Islam Khan I sent a force to take over Bhalwa, which was ruled by Ananta Manikya, another son of Lakshmana Manikya of the Bishwambhar Sur dynasty. The expedition consisted of the forces of Mirza Nuruddin, Mirza Isfandiyar, Haji Shamsuddin Baghdadi, Khwaja Asl, Adil Beg and Mirza Beg, in addition to 500 members of the Subahdar's cavalry. Khan appointed Shaykh Abdul Wahid as the main commander of the entire expedition, which in total was made up 50 elephants, 3000 matchlockers and 4000 cavalry. Ananta Manikya set up defences around Bhalwa with the Magh Raja's assistance, before proceeding forward to the Dakatia banks where he built a fort. The Mughals reached the fort in a few days, and a battle commenced resulting in a number of deaths on both sides. The Bhalwa forces also planned a surprise attack at night. Manikya's chief minister, Mirza Yusuf Barlas, surrendered to the Mughal forces and was rewarded by Abdul Wahid as a mansabdar of 500 soldiers and 300 horses. After losing Barlas however, Manikya did not surrender and rather retreated to Bhalwa at midnight to strengthen the fort there. News of the retreat reached the Mughals two pahars later, and so they began following the Bhalwa forces. Having no time to defend themselves, Manikya retreated further to seek refuge with the Magh Raja Min Razagyi but was defeated at the banks of the Feni River. The Mughals seized all of Manikya's elephants, and Abdul Wahid successfully took control of Bhalwa.