This paper proposes a novel and accurate method for estimating the flight coefficient of a flying disc typically operating at a high rotation rate. In particular, the proposed method introduces a new algorithm that takes advantage of magnetic data measured by a miniaturized sensor module onboard a conventional disc. Since the geomagnetic field measured by the magnetic sensor mounted on the rotating body yields a general sinusoidal waveform, a frequency domain analysis is employed in computing the rotational rate. Furthermore, on the basis of the estimated rate during a whole flight period, a yaw damping derivative coefficient is derived, which enables an accurate prediction of the disc’s flight trajectory. For performance verification, both a reference rotation table test and a real flight test are performed, for which a miniaturized embedded sensor module is designed and manufactured for an onboard flight test. A reference rotation test validates the performance of the proposed method. Subsequently, a flight test, in which a simulator-based trajectory is compared with the true reference trajectory, verifies that the proposed method better predicts the flight trajectory by incorporating the estimated coefficient.