In 1856, his uncle Jackson hired Palmer to work at Westmoreland Coal Company as the secretary and treasurer. The following year he worked at the Pennsylvania Railroad and became private secretary to President John Edgar Thomson, a successful Quaker businessman. At this time, future industrialist Andrew Carnegie was a peer and secretary to a company vice president. Palmer wrote, "Reports of Experiments with Coal Burning Locomotives" and learned about running a railroad from Thomson. Palmer began an evaluation of converting steam engines to run on coal, which was more abundant , rather than wood. His findings were key to changing the type of fuel used to fuel the country's locomotives. He began a relationship with Thomas A. Scott at the Pennsylvania Railroad. Scott was later appointed as Assistant Secretary of War in charge of military transportation during the Civil War.