In 1882, Stoneman was elected governor of California as a Democrat and served a single four-year term. During his tenure, he advocated controlling the rates and limiting the power of the Southern Pacific Railroad; however, he was unsuccessful in his efforts against the railroad-controlled legislature. Stoneman also was a proponent of prison reform, believing prisoners could be rehabilitated through parole. He granted 260 pardons and commuted 146 prison sentences in the last few weeks of his term. Stoneman who was not the Democratic nominee for governor in 1886, left office and retired from public service.