Notable Visayan polities in the pre-colonial period include the following:

• Kedatuan of Madja-as
• Kedatuan of Dapitan
• Rajahnate of Cebu
• Rajahnate of Butuan
• Sultanate of Sulu

The first Filipino people encountered by the Magellan expedition (c. 1521) were Visayans from the island of Suluan; followed by two rulers of the Surigaonon and Butuanon people on a hunting expedition in Limasawa, Rajah Colambu and Rahah Siaui; and finally Rajah Humabon of Cebu. Magellan describes the Suluanon people he encountered as "painted" (tattooed), with gold earrings and armlets, and kerchiefs around their heads. They described Rajah Colambu as having dark hair that hung down to his shoulders, tawny skin, and tattoos all throughout his body. They also noted the large amount of gold ornaments he wore, from large gold earrings to gold tooth fillings. Rajah Colambu wore embroidered patadyong that covered him from the waist to the knees, as well as a kerchief around his head. They also described the boloto (bangka) and the large balanghai (balangay) warships, and the custom of drinking palm wine (uraka) and chewing areca nut. They also described the queen of Cebu as being young and beautiful and covered in white and black cloth. She painted her lips and nails red, and wore a large disc-shaped hat (sadok) made from elaborately-woven leaves.^{[10]: 132–161 [11]}

The 16th century marks the beginning of the Christianization of the Visayan people, with the baptism of Rajah Humabon and about 800 native Cebuanos. The Christianization of the Visayans and Filipinos in general, is commemorated by the Ati-Atihan Festival of Aklan, the Dinagyang Festival of Iloilo, and the Sinulog festival the feast of the Santo Niño de Cebu (Holy Child of Cebu), the brown-skinned depiction of the Child Jesus given by Magellan to Rajah Humabon's wife, Hara Amihan (baptized as Queen Juana). By the 17th century, Visayans already took part in religious missions. In 1672, Pedro Calungsod, a teenage indigenous Visayan catechist and Diego Luis de San Vitores, a Spanish friar, were both martyred in Guam during their mission to preach Christianity to the Chamorro people.^[12]

Visayans, Painting by Filipino painter Damian Domingo

By the end of the 19th century, the Spanish Empire weakened after a series of wars with its American territories. The surge of newer ideas from the outside world thanks to the liberalization of trade by the Bourbon Spain fostered a relatively larger middle class population called the Ilustrados or "the Enlightened Ones." This then became an incentive for the new generation of educated political visionaries to fulfill their dreams of independence from three centuries of colonial rule. Some prominent leaders of the Philippine Revolution in the late 19th century were Visayans. Among leaders of the Propaganda movement was Graciano López Jaena, the Ilonggo who established the propagandist publication La Solidaridad (The Solidarity). In the Visayan theater of the Revolution, Pantaleón Villegas (better known as León Kilat) led the Cebuano revolution in the Battle of Tres de Abril (April 3). One of his successors, Arcadio Maxilom, is a prominent general in the liberalization of Cebu.^[13] Earlier in 1897, Aklan fought against the Spaniards with Francisco Castillo and Candido Iban at the helm. Both were executed after a failed offensive.^[14] Martin Delgado led the rebellion in neighboring Iloilo. Led by Juan Araneta with the assistance of Aniceto Lacson, Negros Occidental was freed while Negros Oriental was liberated by Diego de la Viña. The former would be called the Negros Revolution or the Cinco de Noviembre.^[15] Movements in Capiz were led by Esteban Contreras with the aid of Alejandro Balgos, Santiago Bellosillo and other Ilustrados.^[16][17] Meanwhile, Leandro Locsin Fullon spearheaded the liberalization of Antique.^[18] Most of these revolutionaries would continue their fight for independence until the Philippine–American War. There was also a less heard and short-lived uprising called the Igbaong Revolt which occurred in Igbaong, Antique steered by Maximo and Gregorio Palmero. This revolt, however, was secularly-motivated as they clamored for a more syncretic form of religion based on Visayan animist traditions and Christianity.^[19]

At the peak of the Philippine Revolution, anti-colonial insurgencies sprung from Luzon up to the Visayas. Despite military support from the Tagalog Republic led by Emilio Aguinaldo, Visayan revolutionary leaders were skeptical toward the real motives of the Tagalogs.^[20] Such ethnic animosity was notable to the point that local Visayan leaders demanded forces sent from the north to surrender their armaments and were prohibited to leave revolutionary bases. Moreover, this apprehension led to the full declaration of the Federal State of Visayas on December 12, 1898.^[21] This short-lived federal government, based in Iloilo, was an accumulation of revolutionary movements across Panay and Negros. The following were the elected officials four days prior to the declaration:^[22]

The federation was immediately formed upon the merger of the Cantonal Government of Negros,^[23] the Cantonal Government of Bohol and the Provisional Government of the District of Visayas (based in Panay) which included Romblon. It was said to be based on American federalism and Swiss confederacy. Despite their skepticism towards Malolos, the Visayan government proclaimed its loyalty to the Luzon-based republic while maintaining their own governance, tax collection and army. Apolinario Mabini, then the prime minister of the Malolos republic convinced the Visayan leaders that the Malolos Constitution was only provisional and that the governments in Visayas and Mindanao were promised the power to co-ratify it.^[24][25]

After the 1898 Treaty of Paris, the American colonial government saw the integral part of indigenous elites particularly in Negros in local affairs. This was a different move compared to the previous Spanish imperialists who created a racial distinction between mestizos and native Austronesians (indios). As such, this paved the way for a homogenous concept of a Filipino albeit initially based on financial and political power. These said elites were the hacienderos or the landed, bourgeois-capitalist class concentrated within the sugar cane industry of Negros. The Americans' belief that these hacienderos would be strategic elements in their political hold within the newly acquired colony bolstered the drafting of a separate colonial constitution by and for the sugar industry elites. This constitution likewise established the Negros Cantonal Government. This ensured that the island of Negros would be governed by an indigenous civilian government in contrast to the rest of colonist-controlled areas governed by the American-dominated Philippine Commission.^[26]

During this period, the eastern islands of Samar, Leyte and Biliran (including Marinduque) were directly governed by the Malolos Republic through Vicente Lukban and later by Ambrosio Mojica.^[27] Meanwhile, prior to the full abolition of the federal government on November 12, 1899, Emilio Aguinaldo appointed Martin Delgado as the civil and military governor of Iloilo on April 28, 1899, upon American invasion of Antique. The federal government, much to its rejection of the Cebuano leaders who supported the Katipunan cause, was dissolved upon the Iloilo leaders' voluntary union with the newly formed First Philippine Republic.^[28] Other factors which led to Aguinaldo forcing the Visayans to dissolve their government was due to the federation's resistance from reorganizing its army and forwarding taxes to Malolos.^[29]

Since Philippine independence from the United States, there have been four Philippine Presidents from the Visayan regions: the Cebuano Sergio Osmeña, the Capiznon Manuel Roxas, the Boholano Carlos P. García (who is actually of Ilocano descent through his parents from Bangued, Abra), and the Davaoeño Rodrigo Duterte.

In addition, the Visayas has produced three Vice-Presidents, four Senate Presidents, nine Speakers of the House, six Chief Justices, and six Presidential Spouses including Imelda Marcos, a Waray. The then-president Gloria Macapagal Arroyo is also half Cebuano. Former president Rodrigo Duterte, who is of Visayan ethnicity, also has Leyteño roots. Incumbent president Bongbong Marcos, is of Visayan descent through his Waray mother Imelda Marcos. In international diplomacy the Visayas has produced a United Nations Undersecretary general, the Negros Occidental native Rafael M. Salas who served as the Head of the UNFPA. In the lines of religion, there have been three Visayan Cardinals, namely Julio Rosales from Samar, Jaime Sin from Aklan and Jose Advincula from Capiz. The first Visayan and second Filipino that was canonized is Pedro Calungsod.^[30]

Throughout centuries, non-Visayan groups, most notably migrants from Luzon and foreigners such as the Chinese, have settled in predominantly-Visayan cities in Visayas like Iloilo, Bacolod, Dumaguete and Cebu and Mindanao such as Cagayan de Oro, Iligan, Davao and General Santos.^[31][32] These Filipino-Chinese have been assimilated to mainstream society. One factor would be the limited number of Chinese schools in the Visayas which help maintain the Chinese identity and a stronger sense of a distinct community.^[33] Many of them, particularly the younger generation, have been de-cultured from Chinese traditions, share values about family and friends with other Filipinos, and do not write or speak Chinese well.^[34][35]

Meanwhile, Negritos, locally called Ati, have also been assimilated into mainstream Visayan society.

In Mindanao, migrant ethnic individuals from Luzon as well as Lumad assimilated into a society of Cebuano-speaking majority (Hiligaynon-speaking majority in the case of Soccsksargen) over many years, identifying themselves as Visayans upon learning Cebuano (or Hiligaynon) despite many of them still know and retain their non-Visayan roots and some speak their ancestor's language fluently at least as their second or third languages, since Mindanao is melting pot of different cultures as a result of southward migration from Luzon and Visayas to the island since 20th century. Descendants of these migrant Luzon ethnic groups especially newer generations (as Mindanao-born natives) and Lumad individuals now speak Cebuano or Hiligaynon fluently as their main language with little or no knowledge of their ancestors' native tongues at the time of leaving their respective homelands in Luzon heading south, as for the Lumad, due to the contact with Cebuano- and Hiligaynon-speaking neighbors.^[36]

Visayans have likewise migrated to other parts of the Philippines, especially Metro Manila and Mindanao. The Visayans have also followed the pattern of migration of Filipinos abroad and some have migrated to other parts of the world starting from the Spanish and American period and after World War II. Most are migrants or working as overseas contract workers.