According to one embodiment, a system for measuring coupling misalignment of a rotorcraft drive shaft includes a reference device and a sensor. The sensor is configured to receive a signal from the reference device indicative of a distance between the reference device and the sensor. The reference device and the sensor are configured to be disposed on opposite sides of a flexible coupling coupled to the drive shaft and disposed between the engine and the pylon. The flexible coupling is configured to rotate with the drive shaft and comprises a flexure portion configured to flex in response to a difference in alignment between the engine and the pylon. A misalignment measurement system may be configured to generate a misalignment value in response to the signal.