During the Civil War, Bingham strongly supported the Union and became known as a Radical Republican. President Abraham Lincoln appointed him Judge Advocate of the Union Army with the rank of major during his hiatus from Congress, and Bingham briefly became solicitor of the United States Court of Claims in 1865. Bingham’s judge advocate service was exceptional in the sense that he was a prosecutor or appellate reviewer in three significant military trials. He oversaw critical aspects of the trials of General Fitz-John Porter in 1863, Surgeon General William Hammond in 1864, and the military commission trial of the Lincoln Assassination conspirators in 1864.