Guwahati's history dates back to thousands of years. References in epics, purana's and other traditional histories prove that it is one of Asia's ancient cities. The city of Guwahati was known as Pragjyotishpur in the ancient period, which means the city of eastern astrology. It was a center for research and astrology. Kalika Purana says that present Navagraha Hill was the abode of nine grahas (Planets).

During medieval times between the 12-15th century AD, after the destruction of the Kamata Kingdom, the city lost its earlier glory and became mainly a strategic outpost of the Koch Hajo and Ahom Kingdom of western and eastern Assam. When the western part of the Koch Kingdom fell to the Mughals, the eastern half (Koch Hajo) eventually became a protectorate of Ahom. Although the actual border between both powers (Ahoms and Mughals) fluctuated between the Kartoya River (now in North Bengal) to the Manas and Barnadi rivers, Guwahati remained an important outpost.

 The Chinese Traveler Hiuen Tsang gave a beautiful account of Pragjyotishpur and described the city as a hub of art and culture. He visited during the region of Bhaskar Barman in the 7th Century AD. It is not known when the name Pragjyotishpur changed to Guwahati. According to noted historian Gunaviram Baruah, the presence of large number of guwa (Betel nut) trees gave this particular name. Some other historian says that Guwahati is surrounded by hill so it looks like a cave means guha gave its name. However, During the Ahom rule , this place was named permanently as 'Guwahati'.

  The temples in and around Guwahati describe its ups and downs through ages. Kamakhya, Aswaklanta, Sukreswar, Basisthashram and Umananda are five prominent temples of Guwahati.Hence, it is also known as Panchatirtha (place of five holy shrines). Dighalipukhuri, the rectangular lake in the heart of the city, is the oldest pond of prehistoric period. It is believed that this pond was in the period of Mahabharata. Guwahati was the capital for many kings of ancient Assam like mythological king Narakasur and Bhagadatta.

The Ambari excavations trace the city to the 6th century AD. The city was known as Pragjyotishpura and Durjoya in different time periods, and was the capital under the Barman and the Pala dynasties of the Kamrupa kingdom. The city remained the capital of Assam till the 10-11th century AD under the rulers of the Pala dynasty. Excavations in Ambari, and the brick walls and houses excavated during construction of the present Cotton College's auditorium suggest that it was a city of great size with economic and strategic importance until the 9-11th century AD.

  The city was the seat of the Borphukan, the civil and military authority of the lower Assam region appointed by the Ahom kings. The Borphukan's residence was in the present Fancy Bazaar area and his council-hall, called Dopdar, was situated about 300 yards (270 m) to the west of the Bharalu stream. The Mazindar Baruah, the personal secretary of the Borphukan, had his residence in the present-day Deputy Commissioner's residence. The present campus of Deputy Commissioner of Kamrup was the residential quarters of Borphukan for hundred years. The present residence of Superintendent of Police was the residence of Mazindar Baruah.

The Mughals attacked Assam 17 times and Guwahati was captured many times. The Battle of Saraighat fought close to Guwahati in 1671 is the most well known war, in which the Mughals were over-run due to the strong leadership of Lachit Borphukan and the hard work of the Assamese Army.