Hillyer resigned his captain's commission in November 1863 to become an auditor for the Western & Atlantic Railroad at the request of Governor Joseph E. Brown, who preferred a military man for the role as the railroad was the main supply route for General Joseph E. Johnston's Confederate army. Early in 1864, Hillyer organized the State Road Battalion (consisting mainly of railroad men) and he was placed in command of the defenses of the railroad with the rank of major. Seeing action against cavalry raiders during the Atlanta campaign, Hillyer performed well, but the railroad eventually fell to the Union Army. He and his remaining men surrendered to Federal officers on May 10, 1865.
Legal career and political office
After the war, Hillyer set a law practice in Atlanta with his brother, Henry. The two worked together for a number of years before George eventually joined the law firm of Hillyer, Alexander & Lambdin.
In June 1867, at the age of 32, Hillyer married Ellen Emily Cooley, and together they undertook to raise a family, eventually having 8 children (three of whom died in infancy).