Indoor tracking systems of varying technological complexity are commonly used to quantify physical demands in team-handball. However, there is a lack of research concerning IMU based tracking systems. Therefore, the aim of this study was to evaluate a recent IMU tracking system in team-handball. The evaluation steps included the examination of (i) the agreement between an established LPS+IMU and the IMU tracking system, (ii) the correlation structure of investigated variables, and (iii) differences between training drills using the IMU system. A total of 34 handball players from the female U18 and male U21 national teams of the German Handball Federation participated. Three training sessions including seven training drills and one simulated match were recorded using an established LPS+IMU and the recent IMU tracking system. Results showed that (i) the accumulated player load and time spent in the low speed zone presented substantial agreements (CCC > 0.95), (ii) the accumulated player load was highly correlated with total distance and time spent in very low, low, and very high speed zones (r ≥ 0.61), and (iii) accumulated player loads were highest in training drills covering the entire court. In German junior female and male national handball players, the recent IMU tracking system only allowed a valid assessment of variables that were directly assessed by the measurement technology, i.e., the accumulated player load. However, the player load indicated more the volume than the intensity of training and matches, which should be considered by coaches and scientists when monitoring physical demands in junior handball players.