The history of Farmington can be dated back over 2,000 years ago when the Anasazi "basketmakers" lived in the area in what is now known as "pit houses" and later in pueblo structures built from the native sandstone rock. Their past occupancy can still be seen in the various ruins that fill the surrounding countryside. After the Anasazis exit from the area, the land was then inhabited by the Navajo, Jicarilla Apache and the Utes, which add to the cultural diversity found in this area to this day.

The Spanish passed through this area in the late 1700s and eventually settled in the eastern part of San Juan County in the early 1800s. It was not until mid 1870s that the population of the area began to grow with the actual settlement of what was to become Farmingtown, later shortened to Farmington. Settled by pioneers from Animas City, Colorado at the confluence of the La Plata, Animas and San Juan Rivers. Farmington began to blossom into a flourishing farm and ranch economy and incorporated in 1901.

In the early part of the 1900s, apples became a prime crop for the local farmers. A quote from "The Sunny San Juan Magazine" from 1938 gives us a glimpse into how important the apple commerce was, "The harvesting of some 2,000 acres of fruit calls for a lot of activity in this valley. There are about 53,000 bearing apple trees in the San Juan district. Speaking in terms of commercial apple growing, our valley produces in a normal year in the neighborhood of one hundred standard car loads. Quality of apples compares favorable with the product of other more extensive fruit producing localities. Jonathan, Delicious, Grimes Golden, Rome Beauty and Winesap are the principal varieties, and are harvested in the order named. Thinning is practiced by the successful growers to insure commercial sized apples and to prevent overbearing."

Farmington went through several "oil and gas" booms during the 20th century. At one time, Farmington was the leading oil and gas producing area in the state of New Mexico. The oil and gas industry still remains a staple for the area.