Shelter Valley is a place name located in San Diego County in the U.S. state of California. The town is located along County Route S2, two miles south of its intersection with State Route 78 (known as Scissors Crossing) and 12 miles east of Julian. It lies within the boundaries of the Anza-Borrego Desert State Park and the geologic feature known as Earthquake Valley. The Pacific Crest Trail passes along the northern boundary of the community.