In 1853, a prospector named Christian Kientz discovered rich placer deposits on San Juan Hill. Kientz, an ex-soldier who had fought in Mexico, named the hill after San Juan de Ulloa in Mexico. As miners swarmed into the area to stake their claims, the name of the hill was adopted for the camp that grew nearby. In 1857, the town was granted a post office and "North" was prepended to the name to differentiate it from San Juan in Benito County.

When the placer deposits began to wane, hydraulic mining began in the area with the aid of a series of flumes and ditches hundreds of miles long that brought waters from reservoirs in the Sierra Nevada. Nearby North Columbia saw extensive hydraulic mining.

The world's first long-distance telephone line, built in 1878, ran through North San Juan. At this time, there were ten thousand residents in town. North San Juan began its decline when hydraulic mining was outlawed in 1884.