Around 7000 BC, the ancestors of today's Shibas may have accompanied the earliest immigrants to Japan. Archaeological excavations of the shell mounds left by the Jomonjin, or Rope-Pattern People (named after the pattern found on their earthenware), show that they had small dogs in the 14.5 to 19.5-inch range.

Originally, Shibas were bred to flush birds and small game and were occasionally used to hunt wild boar. Now, they are primarily kept as pets in both Japan and the US. In fact, there are more Shibas in Japan than any other breed.

In the third century BC, a new group of immigrants brought their dogs to Japan. These dogs interbred with the descendants of the Jomonjin dogs, producing canines known for their pointed, erect ears and curly or sickle tails. In the 7th century AD, the Yamato Court established a dog keeper's office, which helped maintain the Japanese native breeds as an integral part of Japanese culture. Although the country was closed to foreigners from the 17th through 18th centuries, some European dogs and a breed known as the Chinese Chin were imported and crossed with native dogs living in more populated areas. However, dogs in the countryside remained relatively pure.

Originally, there were three main varieties of Shiba, each named for its region of origin: the Shinshu Shiba from the Nagano Prefecture, the Mino Shiba from the Gifu Prefecture, and the Sanin Shiba from the northeastern part of the mainland. Although similar, the Shibas from each area contributed to differences in breed type seen today.

From the original Japanese native dogs, six distinct "breeds" in three different sizes developed. They are the Akita (large size), Kishu, Hokkaido, Shikoku, Kai (medium size), and the Shiba (small size). The small-sized dog has been called the Shiba since ancient times, and there are several theories surrounding the development of that name. One popular explanation is that the word Shiba means "brushwood," and the dogs were named for the brushwood bushes where they hunted. Another theory is that the fiery red color of the Shiba is the same as the autumn color of the brushwood leaves. A third conjecture is related to an obsolete meaning of the word Shiba, referring to its small size. These explanations are often combined, and the Shiba is referred to as the "little brushwood dog."

World War II nearly spelled disaster for the Shiba, as most of the dogs that did not perish in bombing raids succumbed to distemper during the post-war years. While the Mino and Sanin Shibas became practically extinct, more of the Shinshu Shibas survived. After the war, Shibas were brought from the remote countryside, and breeding programs were established. The remnants of the various bloodlines were combined to produce the breed as it is known today.

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