The Altiplano Cundiboyacense, where Tunja stands, has held human communities for approximately 12,000 years. Homo sapiens of the Tequendama culture lived in the area by 6375 BCE; archaeologists have recovered their skeletons, including arm bones, from regional sites. By 150 BCE the area around the present city was actively inhabited by people who left abundant material remains. In the first millennium AD, the Muisca arrived - speakers of the Chibcha language who, according to their own tradition, had migrated from Central America through Panama to reach the Andean high plain. They brought their religion, their calendar, and their mythology. One myth holds that the brutal cacique and prophet Goranchacha moved the capital of the northern Muisca from Ramiriquí to Tunja - then called Hunza - and set the political geography that the Spanish would later inherit.

The Muisca Confederation was divided. In the south, the psihipqua - also called the zipa - ruled from Bacatá, near present-day Bogotá. In the north, the hoa ruled from Hunza. The ruler Hunzahúa, brought from Ramiriquí and elected supreme chief of the region, had unified the northern Muisca under the name Hunza. That unity held for generations until the zipa Saguamanchica broke it over a dispute with the cacique of Guatavita. A vast Muisca-on-Muisca war followed. Saguamanchica marched with 50,000 soldiers against hoa Michuá, and the two armies met at what is now remembered as the Battle of Chocontá. Both rulers died in the fighting. A new hoa, Eucaneme, maintained a tense peace until 1514, when the southern psihipqua Nemequene mounted another invasion and was fatally wounded at the Battle of Ventaquemada. When Spanish reports began to filter north in the 1530s, Eucaneme decided to stay in Hunza and sent gifts and peacemakers, hoping to keep the invaders away while he hid his treasures.

Jiménez de Quesada's soldiers took Quemuenchatocha to Suesca to pressure him for the location of more treasure. He abdicated in favor of his nephew Aquiminzaque and returned to Ramiriquí, where he died. Aquiminzaque initially accommodated the Spaniards - he converted to Catholicism, accepted encomienda status under Hernán Pérez de Quesada. Then, in 1540, on the eve of his wedding to the daughter of the cacique of Gámeza, a rumor reached Pérez de Quesada that the ceremony would mask an insurrection. He arrested Aquiminzaque and the assembled caciques of Toca, Motavita, Samacá, Turmequé, and Sutamarchán, and condemned them all to death. Aquiminzaque was beheaded. His death marked the end of the dynasty of zaques of Hunza and the beginning of the dispersal of the Muisca into the encomienda system of the new Tunja Province.

Captain Gonzalo Suárez Rendón founded the Spanish city of Tunja on 6 August 1539 - almost exactly a year after Bogotá's founding - on the lands where Quemuenchatocha had been captured. The main square was laid out with yards for a church and public buildings. By 1550 the city outlines were consolidated, divided into 77 yards with 70 vegetable gardens, 11 estates, and 44 stables. The Franciscans arrived in 1550, the Dominicans the following year, the Augustinians in 1585, the Jesuits in 1611. The Convent of San Agustín rose directly on the ground where Quemuenchatocha had met the conquistadors. In 1616 two parishes were built specifically to receive mestizos and Indigenous residents during the colonial period: Santa Bárbara at the southwest and Las Nieves at the north. On 7 August 1819, Simón Bolívar's forces won the decisive Battle of Boyacá on the Puente de Boyacá, a short ride south of Tunja, ending three centuries of Spanish colonial rule in what would become Colombia.

Here is a fact most visitors to Colombia don't expect: Tunja is among the safest cities in the Americas. According to the International Centre for the Prevention of Crime's 2010 report, it has the lowest homicide rate in Colombia and is below the Latin American average. In 2015 the rate was 2 homicides per 100,000 inhabitants - a figure comparable to the safest European cities and roughly four times lower than the Colombian national average. This is a small city, the capital of Boyacá Department, sitting at 2,820 meters of altitude with a relatively stable economy built on education and government services. Its main university, the Pedagogical and Technological University of Colombia, was founded by General Gustavo Rojas Pinilla - who was himself born in Tunja - and remains one of Colombia's leading public universities. The College of Boyacá, founded on 20 October 1822 by Vice President Francisco de Paula Santander, was the first public school in the territories that later became Venezuela, Ecuador, Panama, and Colombia - back when they were all part of Gran Colombia. Tunja has also fielded two professional football teams, Boyacá Chicó and Patriotas F.C., both playing at La Independencia Stadium, rebuilt to 20,630 seats for the 2009 Copa Libertadores.