Objective. To explore the changes in motivation of Dutch pharmacists for Continuing Education (CE) in the Dutch CE system. Methods. Pharmacists’ motivation was measured across three time points with the Academic Motivation Scale, based on the Self-Determination Theory of motivation. The Latent Growth Modelling technique was used to analyze these data. Results. Over a period of 21 months, Controlled Motivation had increased and Relative Autonomous Motivation of Dutch pharmacists had decreased. Traineeship was the only demographic factor with a significant influence on the change in motivation. No subgroups with different trajectories could be identified. Conclusion. Relative Autonomous Motivation of Dutch pharmacists for CE decreases over time. This indicates a loss of Autonomous Motivation (“good” motivation) in favor of Controlled Motivation (“bad” motivation). Further research needs to be conducted to gain a better understanding of the association between pharmacist motivation and the features of the current CE system.