The purpose of this study was to explore the relationship of problem-based learning (PBL) and the development of critical thinking disposition (CT) and academic achievement in Chinese medical students using a cross-sectional randomized design. Medical students from China Medical University (CMU) were randomized to PBL or non-PBL teaching at the commencement of the study. After five years of study, CT was scored by a Chinese version of the California Critical Thinking Disposition Inventory (CCTDI-CV). The score achieved on a Computer Case Simulation (CCS) test evaluated academic performance. Total CT score was higher in PBL students (n = 170) than non-PBL students (n = 83) (304.7 ± 36.8 vs. 279.2 ± 39.4, p < 0.01). Subscale CT-scores were significant in favor of PBL in six of the seven subscales (truth seeking, open-mindedness, analyticity, systematicity, inquisitiveness, maturity). There was no significant difference in terms of gender on the total CT score, though minor differences were seen in subscales favoring female PBL students. PBL students had higher CCS scores than non-PBL students, but not significantly (112.8 ± 20.6 vs. 107.3 ± 16.5; p = 0.11). There was no significant correlation between CCS scores and CCTDI-CV results. Male students scored slightly higher on the CCS test compared to female students (male 113.4 ± 18.9 vs. female 109.7 ± 19.7), but the difference was not significant. This study concludes that in Chinese medical students, PBL teaching was related to a higher disposition of critical thinking, but not to improved academic skills.