Purpose: The pharmacology and clinical pharmacology and therapeutics (CPT) education during the undergraduate medical curriculum of NOVA Medical School, Lisbon, Portugal, was changed from a traditional programme (i.e. discipline-based, lectures) to a problem-based learning (PBL) programme (i.e. integrated, case-based discussions) without an increase in teaching hours. The aim of this study was to investigate whether this change improved the prescribing competencies of final-year medical students. Methods: Final-year students from both programmes (2015 and 2019) were invited to complete a validated prescribing assessment and questionnaire. The assessment comprised 24 multiple-choice questions in three subdomains (working mechanism, side-effects and interactions/contraindications), and five clinical case scenarios of common diseases. The questionnaire focused on self-reported prescribing confidence, preparedness for future prescribing task and education received. Results: In total, 36 (22%) final-year medical students from the traditional programme and 54 (23%) from the PBL programme participated. Overall, students in the PBL programme had significantly higher knowledge scores than students in the traditional programme (76% (SD 9) vs 67% (SD 15); p = 0.002). Additionally, students in the PBL programme made significantly fewer inappropriate therapy choices (p = 0.023) and fewer erroneous prescriptions than did students in the traditional programme (p = 0.27). Students in the PBL programme felt more confident in prescribing, felt better prepared for prescribing as junior doctor and completed more drug prescriptions during their medical training. Conclusion: Changing from a traditional programme to an integrated PBL programme in pharmacology and CPT during the undergraduate medical curriculum may improve the prescribing competencies of final-year students.