- Sep 1 Isaac Ingalls Stevens, US Union general-major, dies in battle at 44
- Sep 1 Oliver Tilden, of the Bronx, killed in Civil War in Virginia
- Sep 1 Philip "Phil" Kearny, US Union general-major, dies in battle at 48
- Sep 2 Thornton F Brodhead, US lawyer/politician/brigadier general, dies at 40
- Sep 10 Carlos Antonio López, 1st President of Paraguay (1844-62), dies at 71
- Sep 14 Jesse Lee Reno, Union general-major (Reno Nevada), dies at 39
- Sep 14 Samuel Garland Jr, American Brigadier General (Confederate Army), dies in battle at 31
- Sep 17 Lawrence O'Bryan Branch, American Brigadier General (Confederate Army), dies at 41
- Sep 17 William Edwin Starke, Confederate brigadier general, dies in battle at about 48
- Sep 19 [Lewis] Henry Little, American Brigadier General (Confederate Army), dies in battle at 45
- Sep 29 William "Bull" Nelson, Union general-major, murdered after an argument by fellow Union officer General Jefferson C. Davis at 38
- Sep 30 Isaac Peace Rodman, American banker and Brigadier General (Union Army), dies of injury at about 40
Assassination
Car Crash
Hanging
Killed in Action
Plane Crash
Poisoning