Kamakhya Devalaya is inter-mixed with oral history and legends, sometimes these soutrces reflect different periods of time. Mention of Kamakhya has been made in various ancient literatures e.g. Devi Bhagawat, Devi Purana, Kalika Purana, Yogini Tantra, Hevajra Tantra etc. The origin of the Kamakhya Temple is believed to be pre-Aryan or tribal in traits and rituals by many. But religious literature tells us that the original temple was built by Kamdev who regained his beauty here. Built with the help of Bishwakarma, this temple was believed to be a gigantic structure and probably was much bigger than the present one. It was full of beautiful architechtural and sculptural wonder. However, due to some unknown reasons, the upper portion of the temple was completely destroyed. For a long time, the temple lost its importance due to the rise of Shaivism among the rulers and the subject of what was known as Pragjyotisha Kingdom. The Kamakhya Temple’s origin are said to be pre-Aryan.

From the historical point of view, the temple can be presumed to have come into prominence during the reign of King Naraka who is said to be the earliest paramount ruler of the Brahmaputra Valley. But among the successors of Naraka, nothing written or evidential reference of patronage towards the temple is to be found and its history became obsecure till the rise of the Koch Kingdom during the mid 16th Century AD.

Though there is no concrete historical evidence , some researchers drawn conclusion that during 500 C.E. , a beautiful stone temple of Maa Kamakhya was erected in the Nilachal Hill. But perhaps due to natural calamities, the upper part of the original temple was completely destroyed and the lower part was gradually buried.

There are two different views about the reconstruction of the temple during the medieval time. The Koch King Biswa Singha , rebuilt the temple in arounb 1553-54. Afterward, Kalapahar, a muslim invader from Gaur, believed to have destroyed the temple. Many scholars however do not entertain this theory and relate the cause to some kind of natural calamities. The great Koch king Naranarayana who succeeded King Biswa Singha visited this place with his brother Chilarai, they found it in complete ruins. Narayana renovated the temple in 1565 A.D. He also gave royal patronage to the temple.

The political scenario of Assam entered a new phase during the early17th Century. During this period, Ahoms established themselves as the paramount power of the Brahmaputra valley and they started showing keen interest in the temple. There are many stone inscriptions and copper plate to substantiate the involvement of the Ahom Kings with the temple.

The great earthquack of 1897 A.D. caused some damages to the main temple and also mutilated the domes of some other temples of Kamakhya. The royal court of Kochbihar came to the rescue and donated a hefty amount for repairing. Repairing of the temple was also said to be done during various phases in later periods.

The history of Maa Kamakhya Temple is replete with information regarding the royal patronage to the shrine. The names of many of its royal patrons continue to be remembered for their contribution to this great shrine.