In the 14th century, Goddess Karni is said to have lived and performed many miracles during her existence. Karni Mata was a mystic, who led a virtuous life committed to the service of the poor and the oppressed of all communities. The goddess is said to have laid the foundation of Deshnoke. As per the stories, once when her youngest son drowned, Goddess Karni asked Yama (the god of death) to bring him back to life.

Lord Yama replied that he could not return her son's life. Thus, Karni Mata, being an incarnation of Goddess Durga, restored the life of her son. At this point of time, she announced that her family members would die no longer; in fact they would incarnate in the form of rats (kabas) and ultimately, these rats would come back as the members of her family. In Deshnok, there are around 600 families that assert to be the descendants of Karni Mata.

The present temple dates back to the 15th century, when it was built by Maharaja Ganga Singh of Bikaner. The striking façade of the temple is wholly built in marble. Inside the temple complex, one can see a pair of silver doors before the main shrine of the Goddess. These solid silver doors were donated by Maharaja Gaj Singh, on his visit to this temple.

In the main shrine, the image of the goddess is placed with holy things at her feet. Surrounded by rats, Karni Mata is holding a trishul (trident) in one of her hands. The image of Karni Mata is 75 cms tall, decked with a mukut (crown) and a garland of flowers. On her either side, images of her sisters are placed. Karni Mata Temple attracts numerous tourists and pilgrims throughout the year, due to its unique presiding beings.

The temple has around 20,000 rats that are fed, protected and worshipped. Many holes can be seen in the courtyard of this temple. In the vicinity of these holes, one can see rats engaged in different activities. The Rats can be seen here eating from huge metal bowls of milk, sweets and grains. To make the holy rats safe, wires and grills are sited over the courtyard to avoid the birds of prey and other animals.

It is regarded auspicious, if a rat (kaba) runs across one's feet. Even, a glimpse of kaba (white rat) is considered promising and fruitful. Twice a year, a festival is celebrated in the honor of Karni Mata. A grand fair is organized during this time and people come here to seek the blessings of the Goddess.

Bikaner's ruler Ganga Singh had the whole temple built in marble. The domes of the temple are made of silver and gold.

The manadap and the panels above the image are also golden. Devotees place offerings in silver and gold when their prayers are answered.

The elaborate works on the main gate of the temple is a tribute to the fine craftsmanship of the artisans of those days.

On the occasion of Navratri, this temple hosts a fair which attracts hordes of pilgrims from places far the near.