| XF-104 | J65, no gun, no shock cone, short tail. |
| YF-104A | J79-GE-JA or 3B, short tail, no ventral fin. |
| F-104A | J79-GE-3B, short tail. |
| NF-104A | Research variant of the A model fitted with rocket motor above afterburner. |
| QF-104A | Drone version of the A model. |
| F-104B | Two-seat version of the A model, no gun, two canopy types. |
| F-104C | J79-GE-7A, short tail, IRF probe possible. |
| F-104D | Two-seat version of the C model, no gun. |
| F-104DJ | Japanese version of the D model. |
| F-104F | Two-seat trainer used by the German Air Force (Luftwaffe). |
| F-104G | J79-GE-11A, long tail, larger wheels, bulged main wheel doors. |
| TF-104G | Two-seat version of the G model, no gun. |
| RF-104G | Recce version of the G model, no gun, cameras. |
| F-104J | Japanese version, similar to CF-104 except that is has the gun. |
| F-104N | Ex-F-104As and Gs used by NASA. |
| F-104S | J79-GE-19, long tail, ventral fins, larger intakes, no gun, AIM-7 capability. |
| CF-104 | Canadian built version of the G model, narrow main wheels and main wheel doors. Early CF-104s had no gun. |
| CF-104D | Two-seat version of the CF-104. As with the other two-seaters the CF-104D had no gun. |