Born near Newark, Ohio, Atherton attended Denison University, Granville, Ohio, and graduated from Miami University, Oxford, Ohio, in 1853. Later he studied law, and was admitted to the bar in 1855 and commenced practice in Newark, Ohio where he also served as president of the board of education of Newark for fifteen years.
He served as Principal of the local academy at Osceola, Missouri, in 1853 and 1854. Atherton was elected prosecuting attorney of Licking County in 1857 and reelected in 1859 and 1861. While serving as mayor of Newark 1860-1864, he was an unsuccessful Democratic candidate for the State senate in 1863.
He ran for judge of the court of common pleas in 1866, but was unsuccessful.
Atherton was elected as a Democrat to the Forty-sixth and Forty-seventh Congresses (March 4, 1879-March 3, 1883), but afterwards chose not to seek renomination. Atherton was appointed to the Ohio Supreme Court by Governor Hoadly August 20, 1885 to fill a vacancy created by the death of John West. Okey.
He lost election for the remaining two years of Okey"s term that autumn to his Republican opponent, and resigned December 16 of that year. After retiring from the bench, he resumed the practice of law until his death in Newark, Ohio, November 10, 1887.
He was interred in Cedar Hill Cemetery.
Atherton married Margaret A. East. Kumler in Butler, Ohio on November 18, 1856. They had four children.
Other local and national political service included time as member of the city council of Newark for two years and a delegate to the Democratic National Convention at Saint Louis in 1876.