Chichen Itza rose to regional prominence towards the end of the Early Classic period (roughly 600 AD). It was, however, towards the end of the Late Classic and into the early part of the Terminal Classic that the site became a major regional capital, centralizing and dominating political, sociocultural, economic, and ideological life in the northern Maya lowlands. The ascension of Chichen Itza roughly correlates with the decline and fragmentation of the major centers of the southern Maya lowlands

The layout of Chichen Itza site core developed during its earlier phase of occupation, between 750 and 900 AD. Its final layout was developed after 900 AD, and the 10th century saw the rise of the city as a regional capital controlling the area from central Yucatán to the north coast, with its power extending down the east and west coasts of the peninsula.

The earliest hieroglyphic date discovered at Chichen Itza is equivalent to 832 AD, while the last known date was recorded in the Osario temple in 998.

According to some colonial Mayan sources, Hunac Ceel, ruler of Mayapan, conquered Chichen Itza in the 13th century. Hunac Ceel supposedly prophesied his own rise to power. According to custom at the time, individuals thrown into the Cenote Sagrado were believed to have the power of prophecy if they survived. During one such ceremony, the chronicles state, there were no survivors, so Hunac Ceel leaped into the Cenote Sagrado, and when removed, prophesied his own ascension.

In 1526 Spanish Conquistador Francisco de Montejo successfully petitioned the King of Spain for a charter to conquer Yucatán. His first campaign in 1527, which covered much of the Yucatán Peninsula, decimated his forces but ended with the establishment of a small fort at Xaman Haʼ, south of what is today Cancún.

Montejo returned to Yucatán in 1531 with reinforcements and established his main base at Campeche on the west coast. He sent his son, Francisco Montejo The Younger, in late 1532 to conquer the interior of the Yucatán Peninsula from the north. The objective from the beginning was to go to Chichén Itzá and establish a capital.

The Maya became more hostile over time, and eventually they laid siege to the Spanish, cutting off their supply line to the coast, and forcing them to barricade themselves among the ruins of the ancient city. Months passed, but no reinforcements arrived. Montejo the Younger attempted an all out assault against the Maya and lost 150 of his remaining troops. He was forced to abandon Chichén Itzá in 1534 under cover of darkness. By 1535, all Spanish had been driven from the Yucatán Peninsula.

Montejo eventually returned to Yucatán and, by recruiting Maya from Campeche and Champoton, built a large Indio-Spanish army and conquered the peninsula. The Spanish crown later issued a land grant that included Chichen Itza and by 1588 it was a working cattle ranch.

In 1894 the United States Consul to Yucatán, Edward Herbert Thompson, purchased the Hacienda Chichén, which included the ruins of Chichen Itza. For 30 years, Thompson explored the ancient city. His discoveries included the earliest dated carving upon a lintel in the Temple of the Initial Series and the excavation of several graves in the Osario (High Priest's Temple).

In 1923, the Mexican government awarded the Carnegie Institution a 10-year permit (later extended another 10 years) to allow U.S. archaeologists to conduct extensive excavation and restoration of Chichen Itza. Carnegie researchers excavated and restored the Temple of Warriors and the Caracol, among other major buildings. At the same time, the Mexican government excavated and restored El Castillo (Temple of Kukulcan) and the Great Ball Court.

In 1926, the Mexican government charged Edward Thompson with theft, claiming he stole the artifacts from the Cenote Sagrado and smuggled them out of the country. The government seized the Hacienda Chichén. Thompson, who was in the United States at the time, never returned to Yucatán. He wrote about his research and investigations of the Maya culture in a book People of the Serpent published in 1932. He died in New Jersey in 1935.

There have been two later expeditions to recover artifacts from the Cenote Sagrado, in 1961 and 1967. The first was sponsored by the National Geographic, and the second by private interests. Both projects were supervised by Mexico's National Institute of Anthropology and History (INAH). INAH has conducted an ongoing effort to excavate and restore other monuments in the archaeological zone, including the Osario, Akab Dzib, and several buildings in Chichén Viejo (Old Chichen).