Humphreys was commissioned a captain in the Confederate Army in 1861 and was subsequently promoted to brigadier general after the Battle of Gettysburg in 1863.
In October 1865, he was elected as a Democrat and sworn in as the 26th governor of Mississippi under President Andrew Johnson's Reconstruction plan. He won re-election in 1868 and continued with a second term, but with the beginning of Congressional control of Reconstruction he was physically removed by occupying U.S. armed forces on June 15 of that year. Afterwards, he entered a career in insurance in Jackson, Mississippi. He continued there until his retirement in 1877 to his plantation where he died in 1882.
Humphreys County, Mississippi is named after him. His son, also named Benjamin G. Humphreys, entered into a political career of his own.