He retired from the Army as a lieutenant colonel in 1882, due to illness. Williamson had suffered from bad health for the last 20 years of his life and died of tuberculosis in San Francisco, California. He was buried at the Masonic Cemetery in San Francisco. Mount Williamson in California, a western woodpecker, the Williamson's sapsucker, and Williamson Mountain and the Williamson River in Oregon are named in his honor.