The present disclosure provides methods and systems for fault detection for a speed sensing system of a multi-engine rotorcraft. A shaft speed for a first engine and a rotor speed for at least one rotor of the multi-engine rotorcraft are obtained. The shaft speed is compared to the rotor speed. When the shaft speed is greater than the rotor speed, a first fault in the speed sensing system is detected and a first speed sensing system fault signal is issued. When the shaft speed is less than the rotor speed, a determination is made regarding whether the first engine is coupled the at least one rotor based on a fuel flow to the first engine. A second fault in the speed sensing system is detected and a second speed sensing system fault signal is issued responsive to determining that the first engine is coupled to the at least one rotor.