Nephi is located at the mouth of Salt Creek Canyon; the north peak of Mount Nebo is to the northeast and the Red Cliffs are to the southeast. The city covers an area of approximately four square miles.

As with most settlements in Utah, Nephi's founders were Mormons, and the name of the town came from the Book of Mormon. In the summer of 1851 Joseph L. Haywood and Jesse W. Fox, the territorial surveyor, were instructed by church leaders to lay out the town of Salt Creek, so named for the local salty stream. Haywood served as civic and spiritual leader in the area for three years. The settlers immediately began to clear ground and build homes. They also started schools for their children. Nephi boasted the third high school (and the first rural one) in the state in 1894. In 1879 a Presbyterian school was opened and later a Methodist school.

Nephi was known for some years as Salt Creek. However, early church records refer to it as the Nephi Branch and some government records also called it Nephi. Until 22 May 1882 mail to the town was addressed to the Salt Creek post office. Nephi was incorporated in 1889, and on 16 January 1882 an act by the governor and the legislature of the territory was approved, making Nephi the county seat of Juab County.

Agriculture was the first industry. Farming and livestock have always been important in the Nephi area. The settlers traced the source of the salt in the creek to a cave in the canyon east of town and they then began to mine it. This soon became a flourishing local industry, with salt traded to people as far away as St. George in exchange for food and clothing. In 1893 the Nebo Salt Manufacturing Company was organized. However, it eventually became unprofitable to compete with the larger companies on the shores of the Great Salt Lake, and 1925 marked the end of the local industry.

Milling was another local industry with Zimra H. Baxter, George W. Bradley, and Abraham Boswell building a grist mill. Later more mills were built and modernized, and Nephi's Gem and Snowflake flour became known throughout most of Utah. In 1917 R.C. and Robert Winn built a mill which was later purchased by the Hermanson family. In June 1991 it was destroyed by fire with a loss of more than $20,000 worth of inventory; however, the California partners who now own it are planning to rebuild.

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