Stewart was born in Wayne County, New York. As a child he moved with his parents to Trumbull County, Ohio. As a young man he was a mathematics teacher in Ohio. In 1849 he began attending Yale University but left in 1850 to move to California. Like many young men during that time, he came to California because of the Gold Rush. He arrived in San Francisco, California and soon left to begin mining near Nevada City, California. In 1852 he stopped mining and decided to become a lawyer in Nevada City. He almost immediately became a district attorney, and servd as attorney general of California briefly during 1854, at the age of 27.

In 1860 Stewart moved to Virginia City, Nevada where he participated in mining litigation and helped the development of the Comstock lode. As Nevada was becoming a state in 1864, he helped the state develop its constitution.

In 1864, Stewart was elected to the United States Senate as a Republican. He served in the Senate until 1875 when he decided to retire and began to practice law again in Nevada and California. He was elected to the Senate again in 1887 and reelected in 1893 and 1899. During the 1890s he left the Republican Party to join the Silver Republicans, a faction which supported the Free Silver movement.

Stewart retired from the Senate in 1905. he remained in Washington D.C. and died there four years later. He was cremated and the ashes are kept in Laurel Hill Cemetery in San Francisco.