This study aimed to (a) develop an algorithm that could estimate a baseball bat trajectory from the beginning of the swing to the follow-through phase during a practice swing without a ball and (b) evaluate the accuracy of the proposed method using a three-dimensional motion capture system. The sensor fusion using the adaptive Kalman filter for compensating velocity decreased the error of acceleration integration during the follow-through phase. Further, the three-dimensional bat trajectory in a global coordinate was estimated by combining the sensor fusion and compensation by motion characteristics. The three-dimensional bat trajectory from the swing beginning to the follow-through phase estimated by the proposed method was compared with the three-dimensional bat trajectory obtained by the three-dimensional motion capture system. The proposed method achieved a root mean square of the error of 7.72 km/h for velocity, which was less than the root mean square of the error (8.91 km/h) obtained by simple time integration of forward direction. These results indicate that the error by acceleration integration during the follow-through phase is compensated. The proposed method is, thus, deemed effective and can be used to evaluate baseball swing, including the follow-through phase, with high accuracy.