Long before Patani bore its name, a Hindu-Buddhist kingdom called Langkasuka occupied this stretch of the Malay Peninsula. Founded as early as the second century, Langkasuka appeared in Chinese travelers' accounts and drew trade from across the region as a stopping point for ships crossing the Gulf of Thailand. The Buddhist pilgrim Yijing recorded his visits. By the sixth and seventh centuries, Langkasuka had reached its peak as a commercial center, but decline followed as the waterway linking it to the sea silted up and political circumstances shifted. The most substantial ruins believed to be ancient Langkasuka lie at Yarang, about fifteen kilometers from the modern city of Pattani. How Langkasuka became Patani is unknown. The Javanese text Nagarakretagama, written in 1365, mentions Langkasuka but not Patani, suggesting the sultanate had not yet emerged. According to the Hikayat Patani, Patani's predecessor was Kota Mahligai, the citadel town, whose ruler founded Patani sometime between 1350 and 1450.

The early sultanate was shaped by its relationship with Siam. Patani's first rulers converted to Islam, taking the title Sultan Ismail Shah or Mahmud Shah, and the Portuguese arrived to trade by 1516. Raja Mahmud in the mid-sixteenth century was regarded as ruling justly, bringing development to the region. But it was Sultan Mudhaffar Shah who made the most dramatic move. In 1563, angry over his unwelcome reception at the Thai court, he attacked Ayutthaya itself. King Chakkraphat fled the capital for two months, though Mudhaffar ultimately failed to take the throne. He died suddenly in 1564 on his way home. His brother Manzur Shah, who had been left in charge, assumed rule over a sultanate that had proved its willingness to challenge even the great Siamese kingdom.

The age of the queens began with bloodshed. Sultan Bahdur, remembered as a tyrant, was the last male ruler of the inland dynasty. His sister, Raja Hijau, took the throne in 1584 and presided over Patani's golden age. Under her rule, the port attracted merchants from across the known world. A 1603 Dutch report by Jacob van Neck estimated that the Chinese population of Patani rivaled that of the native Malays and dominated the city's commerce. The English East India Company established a trading post, though it withdrew after its chief factor, John Jourdain, was killed off the Patani coast by the Dutch in 1619. Raja Ungu, the Purple Queen, was particularly fierce in resisting Siamese interference. But by the time Raja Kuning, her daughter, assumed the throne in 1635, the queens' authority was eroding. When Patani joined other tributary states in rebelling against Ayutthaya in 1646, it was subdued, and five decades of political disorder followed.

Foreign merchants abandoned Patani as lawlessness spread and local rulers proved unable to restore order. By the end of the seventeenth century, Chinese sources described the once-great port as sparsely populated and barbaric. The throne sat vacant for decades. In 1786, Siam invaded and took effective control. Britain formally recognized Siamese ownership in the Burney Treaty of 1826. A partial revival came in 1842, when a member of Kelantanese royalty reclaimed the throne, and for sixty years the sultanate maintained a delicate balance between nominal independence and Siamese suzerainty, paying the traditional bunga mas tribute of golden flowers. But Siam's patience had limits.

In 1902, Siam demanded administrative reforms that would have effectively ended Patani's autonomy. Sultan Abdul Kadir Kamaruddin Syah, the last raja, refused. Siam arrested and deposed him, ending over four centuries of Malay rule in the region. The territory was absorbed into what would become Thailand's southern provinces of Pattani, Yala, and Narathiwat, where a Malay Muslim population remains to this day. The descendants of the last raja went on to prominence in Malaysia: his granddaughter Tengku Budriah became Queen Consort of Perlis. The kingdom itself exists now only in the Hikayat Patani, in the ruins at Yarang, and in the unresolved tensions of Thailand's deep south, where the memory of Patani's independence has never fully disappeared.