John Wagner may refer to:
- John Wagner (born 1949), American-born British comics writer
- John A. Wagner (1885–1964), Michigan politician
- John C. Wagner (1858–1937), American politician and businessman
- John D. Wagner, American author and businessman
- John P. Wagner (1874–1955), American baseball shortstop
- John W. Wagner, (1837–1896), Union Army soldier in the American Civil War who received the Medal of Honor