Long before European settlement, the area was regularly explored by the Anasazi, and later the Utes, who hunted and lived in the San Juans during the summer.

[3] Permanent settlement in the area surrounding present-day San Juan County began in 1860, near the end of the Colorado Gold Rush.

These first settlers were a group of prospectors led by Charles Baker, who made their way into the San Juan Mountains searching for gold.

The region boomed after George Howard and R. J. McNutt discovered the Sunnyside silver vein along Hurricane Peak, outside the mining camp of Eureka.

Gold was then discovered in 1882, which helped the county weather the Panic of 1893 far better than other mining communities, such as Aspen or Creede.

[8] The SJDMA refused to consider any reduction in hours or increase in wages, helping to provoke a bitter strike.

The Sunnyside mine was shut down after the 1929 stock market crash, but was acquired by Standard Metals Corp. in 1959, and reopened, finding gold in 1973 with the Little Mary vein.

The county's economy was dealt a devastating blow in 1992 when the mine and the corresponding Shenandoah-Dives mill, the last operating in the region, permanently closed.

As of 2013, 33% of residents walked to work, 18% drove alone, 19% carpooled, and 18% bicycled, though the small population size introduces considerable margins of error to these statistics.