Abstract Background Clinical pharmacists must have a complex combination of academic knowledge and practical experience that integrates all aspects of practice. Taiwanâ s Ministry of Health and Welfare in 2007 launched the Postgraduate Year (PGY) training program to increase the standard of pharmaceutical care. This study aims to develop a pharmacist-specific Chinese-language Mini-Clinical Evaluation Exercise (Mini-CEX) to evaluate the professional development of postgraduate year trainees. Method The specialized Mini-CEX was developed based on the core competencies of pharmacists, published literature, and expert opinion. A pilot test and evaluator workshop were held prior to the administration of the main test. Fifty-three samples were recruited. The main study was conducted at two regional teaching hospitals and a medical center teaching hospital in Taiwan between February and June 2012. The results were analyzed with the kappa statistic (inter-rater reliability) and descriptive statistics, while the Kruskal-Wallis test was used to examine the PGY traineesâ Mini-CEX scores based on their performances. Results Trainees who had recently completed PGY programs (C-PGY) and 2nd year PGY trainees (PGY2) earned excellent scores, while the 1st year PGY trainees (PGY1) earned satisfactory scores in overall performance. C-PGY and PGY2 trainees also performed significantly better than PGY1 trainees in the organization and efficiency domain, and the communication skills domain. Conclusion This study demonstrates the feasibility of using the newly developed pharmacist-specific Chinese-language version of the Mini-CEX instrument to evaluate the core competencies of PGY trainees in clinical settings.