It is said to have been founded by Sunan Gunungjati, as marked by his letter proclaiming Cirebon's independence from Pajajaran in 1482,[2] although the settlement and the polity had been established earlier, in 1445.

According to Sulendraningrat, who based it on the Babad Tanah Sunda script,[3] and Atja who based it on the Carita Purwaka Caruban Nagari script, Cirebon was at first a small hamlet built by Ki Gedeng Tapa, which eventually developed into a bustling port village named Caruban (Sundanese for "mixture"), because the port town was a melting pot settled by immigrants from various ethnic groups, religions, languages, customs, and livelihoods.

Another theory suggests that the town's name is derived from rebon, the Sundanese word for small shrimp that live in the area.

Initially, a common livelihood in the settlement was fishing and collecting rebon along the coast, making shrimp paste or petis udang from it.

The village of Muara Jati was in the coastal area around the port of Cirebon and was part of the Sunda Kingdom, as stated in the travel records of Prince Bujangga Manik, a Hindu Sundanese hermit who visited several Hindu sites in Java and Bali in the late 15th century or early 16th century.

The transformation from a small Hindu coastal fishing village into a thriving Muslim port began with the rule of Ki Ageng Tapa.

The West Java region including Muara Jati belonged to the Sunda Kingdom, with its capital in Pakuan Pajajaran.

In 1442 Prince Walangsungsang married Nyai Endang Geulis, daughter of Ki Gedheng Danu Warsih from the Gunung Mara Api hermitage.

After Ki Gedeng Alang-Alang died in 1447, Walangsungsang was appointed as the ruler of the town and established a court, and assumed a new title as Prince Cakrabuana.

He asked his uncle, Tumenggung Sri Mangana (Cakrabuana) to establish an Islamic school in Caruban or Carbon.

He is popularly known with his posthumous name, Sunan Gunung Jati; he ascended the throne as Sultan Carbon I and resided in Keraton Pakungwati.

In 1482 Sharif Hidayatullah sent a letter to his grandfather King Siliwangi, stating that Cirebon refused to pay tribute to Pajajaran.

The Cirebon independence proclamation was marked with Chandrasengkala (chronogram) Dwa Dasi Sukla Pakca Cetra Masa Sahasra Patangatus Papat Ikang Sakakala, which corresponds to 2 April 1482.

It was likely his son, Hasanudin, who commanded this military operation in 1527, just as the Portuguese fleet was arriving on the coast at Sunda Kelapa, to capture these towns.

Ulamas from his court and mosque spread Islam to inland Majalengka, Kuningan, Kawali (Galuh), as well as the neighbouring coastal ports of Sunda Kelapa, and Banten.

Three years later the king died and was buried in Gunung Sembung cemetery, 5 km north of the town centre of Cirebon.

Around 1617 Agung launched his westward campaign targeted against Dutch settlements in Batavia, and rallied his massive troops near Cirebon's border.

However the Sundanese Priangan menak (nobles) of Sumedang and Ciamis, suspected that Agung's campaign was in actuality a strategy to occupy their lands.

Mataram, on the other hand, suspected that Cirebon was not sincerely cementing the alliance with their Central Javanese counterpart since Panembahan Adiningkusuma and Sultan Ageng Tirtayasa of Banten belonged to the same Sundanese Pajajaran lineage.

Prince Wangsakerta assumed the everyday administration, but was worried about the fate of his elder brothers being held as hostages in the Mataram court.

Because of this incident, the Cirebon succession was also held hostage by Mataram, and by their own grandfather Amangkurat I. Wangsakerta went to Banten to seek Sultan Ageng Tirtayasa's help to free his brothers.

Taking advantage of the outbreak of the Trunojoya rebellion against Mataram, Sultan Ageng Tirtayasa secretly supported the revolt and managed to save the two Cirebon princes.

One of the princes, Pangeran Raja Kanoman, demanded his share of the throne and separated the kingdom by forming his own called Kesultanan Kacirebonan.

Since 1619, the Dutch East India Company had firmly established their base in Batavia, and since the 18th century, the inland mountainous region of Priangan had also been under their possession, ceded from Banten and Mataram.

The sultanates' authority was officially disbanded by the Dutch East Indies government through the establishment of Gemeente Cheribon (Cirebon Municipality), which consists of 1,100 hectares, with around 20,000 inhabitants.

Similar to the Dutch East Indies colonial era, the royal houses (the Kasepuhan, Kanoman, Keprabonan, and Kacirebonan kratons) only held ceremonial status as a local cultural symbol.

In 2012, the government planned to restore the four keratons, or palaces, in Cirebon—the Kasultanan Kasepuhan, Kanoman, Kacirebonan, and Keprabonan palaces—which by then are still in various stages of ruin.

The royal carriage of Kasepuhan's Singa Barong and Kanoman's Paksi Naga Liman resembles the mixture of three animals; eagle, elephant, and dragon, to symbolize Indian Hinduism, Arabic Islam, and Chinese influences.

The images of Macan Ali, Singa Barong, and Paksi Naga Liman are also often featured as patterns in Cirebon batik.

In 1679 the Sultanate of Cirebon was divided into two kingdoms, namely Kasepuhan and Kanoman, due to the struggle for power between the brothers.