In pharmacology teaching, pharmacokinetics (PK) and pharmacodynamics (PD) may be defined as part of the ‘general pharmacology’ domain, whereas effects of drugs on the autonomic nervous system and clinical trial design might be defined as part of the ‘medical’ and ‘clinical’ pharmacology domain, respectively. We recently designed a pharmacology course covering these domains for second year Health and Life Sciences students at the Vrije Universiteit Amsterdam (VU). We used a combination of lectures, problem-based learning and practicals to transfer knowledge to students in order for them to acquire sufficient knowledge and insight to solve real-world pharmacological problems. To evaluate whether we 1) successfully aligned our course objectives with both our teaching strategy and assessment, and 2) to identify topics in our course that would benefit from improvement in teaching strategy and/or effort, we determined success rate of the exam questions in above-defined pharmacology domains. We analyzed 3 consecutive second year cohorts (n = 377) of students enrolled in our course, and found a statistically significant reduction in success rate in exam questions of the general pharmacology domain (especially in PK), compared to domains covering ‘medical’ and ‘clinical’ pharmacology. In addition, we found lower success rates for ‘knows how’ questions compared to ‘knows’ questions in the combined PK/PD domain. Our data show that we overall succeeded in aligning our course objectives with both our teaching strategy and assessment, but that outcomes on the PK domain might benefit from additional attention.