Due to silting of the Mestizo River, Vigan is no longer separated from the mainland, therefore no longer an island. The city is unique in the Philippines because it is one of many extensive surviving Philippine historic cities, dating back to the 16th century.

Vigan was a coastal trading post long before the Spaniards arrived; Chinese traders sailing from the South China Sea came to Isla de Vigan (Island of Vigan) via the Mestizo River that surrounded it. On board their ships were seafaring merchants who came to trade goods from other Asian kingdoms in exchange for gold, beeswax, and other mountain products brought by the indigenous peoples from the Cordillera region.

In the book The Philippine Island (Vol. III, p. 276, Blair and Robertson) two letters from Governor-General Guido de Lavezaris to King Philip II of Spain mention: "It seemed best to send Captain Juan de Salcedo with 70 or 80 soldiers to explore the coast of Los Ilocanos on the shores of the river called Bigan." The Spaniards led by Salcedo marched north from Manila on May 20, 1572. They arrived in Vigan on June 13, 1572.[1]

Thus, after the successful expedition and the exploration of the North, Juan de Salcedo founded "Villa Fernandina de Vigan" in honor of King Philip II's son, Prince Ferdinand, who died at the age of four. From Vigan, Salcedo rounded the tip of Luzón and proceeded to pacify Camarines, Albay, and Catanduanes. As a reward for his services to the King of Spain, Salcedo was awarded the old province of Ilocos, which consisted of the modern provinces of Ilocos Norte, Ilocos Sur, Abra, La Union and part of Mountain Province as his hacienda (estate), and was accorded the title of Justicia Mayor de esta Provincia de Ylocos (Province Mayor of Ilocos).[2][3]

In 1574, Salcedo returned to the capital of his encomienda (trusteeship), Vigan, bringing with him his soldiers and some Augustinian missionaries to pioneer the evangelization of the Ilocos region. He established a Spanish city for the purpose of controlling the neighboring country.

Governor General Gómez Pérez Dasmariñas, in his account of encomienda dated in Manila on May 31, 1591, states: "The town of Vigan called Villa Fernandina consisted of Spanish settlers; a priest; a Justice Alcalde Mayor (Governor); and a Deputy. The King collects 800 tributes (equivalent to 3,200 subjects)." During this period, Vigan was composed of 19 barrios (districts).

Between 1645 and 1660, Vigan was divided into 21 Cabezas de Barrio (Town Mayors) as mentioned in the Libro de Casamiento (Book of Marriage); from the records of the parish house of Vigan found in its archives. Separated from the indigenous population, the Chinese migrants were residents in a neighbourhood called El Pariancillo, los Sangleyes del parian (The Sangleyes of the Parian); and the Spanish settlers were residents in a town called Los Españoles de la Villa (The Town Spaniards). The Spaniards consisted of about 60 Spanish Households.[4]

In 1755, Bp. Juan de la Fuente Yepes made a request to the King Fernando VI to move the Diocese of Nueva Segovie to Villa Fernandina due to the deteriorating status of Lal-lo. In 1758, with the Royal Decree signed by Fernando VI, Villa Fernadina became Ciudad Fernandina de Vigan and the See of Nueva Segovia was transferred from Lal-lo, Cagayan. The bell ensconced within the belfry of Vigan, has the imprinted words of the decree. Wherever the clang of the bell reaches, it marks the territory of Ciudad Fernandina de Vigan.

During the Philippine Revolution, revolutionary forces under Manuel Tinio, supported by the Ilocano rebels, attacked and defeated the Spanish colonial forces and captured the city in the Siege of Vigan.[5] During the Philippine–American War, American forces led by Commander McCracken and Lt. Col. James Parker occupied the town in Nov. 1899.[6]

At the start of World War II, Vigan was one of the first places in the Philippines invaded by Japan on December 10, 1941. In 1945, combined U.S. and Philippine Commonwealth ground troops, aided by Ilocano resistance fighters, defeated the Japanese Imperial forces and liberated Vigan.

In 1999, Vigan was listed by UNESCO as the best preserved example of Spanish colonial towns in Asia.[7] Its architecture is the conglomeration of cultural elements from the Philippines, China, and Spain, making it unique in the world.

On December 27, 2000, then President Joseph Estrada signed Republic Act No. 8988, that "revalidated and recognized" Vigan's city status granted by virtue of the Royal Decree of September 7, 1757, issued by Ferdinand VI, King of Spain.[8] This legislation serves as Vigan's present city charter. The charter did not provide a clause for a plebiscite and the law took effect in January 2001.

On December 7, 2014, Vigan was named as one of the New7Wonders Cities.[9]

On July 27, 2022, a 7.0 magnitude earthquake struck parts of Luzon,[10] damaging the city's UNESCO World Heritage sites including the Vigan Cathedral and old-century houses, as well as few power lines toppled along Calle Crisologo.[11]