Born near Newark, Ohio, Atherton attended Denison University, Granville, Ohio, and graduated from Miami University, Oxford, Ohio, in 1853. He served as Principal of the local academy at Osceola, Missouri, in 1853 and 1854.
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.
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. 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 St. Louis in 1876.
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. After being an unsuccessful candidate for judge of the Ohio Supreme Court in 1882, he was appointed to that position by Governor Hoadly the same year and served until the election of his successor six months later.