After his graduation from Yale in 1854, he entered the service of the United States Coast Survey, and from 1859 to 1866 had charge of the Magnetic Observatory at Key West, Florida.
Upon completion of his series of magnetic observations, he resigned on May 15, 1866, receiving high praise for his work from his superiors.
On June 18, 1866, he was appointed prosecuting attorney in the county criminal court in Key West.
During the autumn of 1876, Walker suffered a stroke of paralysis, and ailed from nervous debility thereafter.
In May 1881, he went north to visit his relatives, and arrived in Downington just a month before his death at the age of fifty-five, which occurred at his sister's house in that town on June 9, 1881.