Originally named Birchville, after prospector Robert H. Birch, one of three finding the first gold, it later took the Spanish name Pinos Altos, meaning tall pines, because there were tall trees growing in the area. These were cut down as the town grew to have a population of about 9,000 during the 1880s and 1890s before slowly being abandoned during the early 1900s. Today, many of the original buildings remain.
From the discovery of gold in 1860 until late 1861, miners were harassed by Apache Indian opposed to European American settlers occupying their lands. On September 27, 1861, it was the site of the Battle of Pinos Altos between the Arizona Guards of Pinos Altos, a Confederate Arizona Territorial militia company, and Apache warriors led by Mangas Coloradas and Cochise. This battle did not end the conflict between European American settlers and Native Americans, which continued for several years, with neither side particularly willing to see the dispute resolved peacefully. Even when a treaty was eventually negotiated between the settlers and Indians, a settler hosting a dinner to celebrate the signing opened fire on 60 unarmed Indians, killing and injuring many of those assembled. Indian hostility continued until the military built forts to protect the settlement in 1869.