San Juan County is a county located in the U.S. state of New Mexico. As of the 2010 census, the population was 130,044, making it the fifth-most populous county in New Mexico. Its county seat is Aztec. The county was created in 1887.San Juan County is part of the Farmington, NM Metropolitan Statistical Area. It is located in the northwest corner of the state and includes the New Mexico portion of the Four Corners.