Fowler was born in Steubenville, Ohio. He graduated from Grove Academy in that city and subsequently from Franklin College in New Athens, Ohio in 1843. He taught school in Shelby County, Kentucky in 1844. He served as a professor of mathematics at Franklin College in Davidson County, Tennessee from 1845 to 1849. He studied law in Bowling Green, Kentucky and was subsequently admitted to the bar and practiced in Tennessee until 1861. He also served as president of Howard Female College in Gallatin, Tennessee from 1856 to 1861.

Fowler was an ardent Unionist. The Biographical Directory of the United States Congress states that he was the State Comptroller of Tennessee from 1862 until 1865. The official Tennessee Blue Book states that the holder of that office during this period was "Joseph S. Foster". It is likely that the Biographical Directory is the correct source; the Confederate state government of Tennessee was never very effective and largely disfunctional due to the early loss of much Tennessee territory to Union forces by the Confederates and also due to the fact that neither the Confederacy nor slavery had ever had much public support in East Tennessee. Most of the state was under the control of the Union military government of Abraham Lincoln's appointed governor, Andrew Johnson, for most of the duration of the American Civil War; his government was fairly functional and it is likely that Fowler served this regime as Comptroller and that the Blue Book records his name erroneously.

In 1866 Tennessee became the first former Confederate state to be readmitted to the Union; the Tennessee General Assembly elected Fowler to the Senate, where his service began on July 24, 1866. Fowler became a part of the majority Republican caucus. In the 40th Congress he served as chairman of the Committee on Engrossed Bills.

He did not seek a subsequent term in the Senate upon the expiry of his term in 1871. He also did not return to Tennessee to live, but remained in Washington DC, practicing law there until shortly before his death in 1902.