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The central icon of Vimala is of the sixth century CE. Based on its architecture, the present structure seems to have been built in the ninth century under the Eastern Ganga dynasty, possibly over ruins of an earlier temple. Its architecture is similar to the shrine of Narasimha near the Mukti-mandapa (a temple hall) in the Jagannath temple complex, dated to the ninth century. The Madala Panji states that the temple was constructed by Yayati Keshari, a ruler of the Somavashi Dynasty of South Kosala. Kings Yayati I (c. 922–955) and Yayati II (c. 1025–1040) are known by Yayati Keshari. The sculptures, especially the parshvadevatas (attendant deities) and the central icon's background slab reflect the Somavashi style. They may be part of the original temple, on whose ruins the new temple was constructed. Vimala is believed to have preceded even the central Jagannath shrine.

Hindu philosopher and saint Adi Shankara (c. 8th century) are believed to have established Govardhana matha in Puri, with Vimala as its presiding goddess. According to Starza (author of The Jagannatha Temple at Puri), the Jagannath Temple was once a center of worship for the Trimurti of Brahma, Vishnu, and Shiva, along with their consorts and the three central forms of the Hindu Goddess, Sarasvati, Lakshmi and Parvati (in the form of Vimala). The Shri Vidya sect devoted to Goddess worship was strong here until the 17th century. Slowly, Shri Vidya and Shiva-centric Shaiva traditions were eroded, but remnants continue, with the Vishnu-centric Vaishnavism becoming the sole tradition. The Tantric Panchamakara, which includes fish, meat, liquor, parched grain, and ritual intercourse, were replaced with vegetarian offerings and devadasis dance. Fish was caught locally and offered to the goddess.[4] King Narasimhadeva, who ruled between 1623–47, ended the goddess's meat and fish offerings,[3] although the tradition was later partly revitalized. Today, the goddess is offered meat and fish on special days.

The temple is located in the south-west corner of the inner enclosure of the Jagannath temple complex and on the right-hand western corner of the tower of Jagannath, next to the sacred pond Rohini Kunda. The temple faces east and is built of sandstone and laterite. It is built in the Deula style that has four components, namely, vimana (structure containing the sanctum), Jaganmohan (assembly hall), Nata-Mandapa (festival hall), and Bhoga-Mandapa (hall of offerings). The temple is maintained and was renovated around 2005 by the Archaeological Survey of India, Bhubaneswar Circle.