The purpose of this research was to investigate the effect of problem-based scenario method with experiments on the biology self-efficacy and critical thinking tendency of the prospective science teachers. In the study, pre-test and post-test experimental design without any control group was used. The participants of the research were 108 second-grade prospective science teachers in an university in the west of Turkey. Throughout 12 weeks, prospective teachers were given scenarios and they designed experiments based on these scenarios in the Biology Laboratory II course. The biology self-efficacy scale and critical thinking tendency scale were used as a pre-test and post-test. In the analysis of data, Wilcoxon Signed-Rank Test for paired samples was used through SPSS-21. The findings showed that there was a statistically significant difference between biology self-efficacy scale pre-test and post-test of prospective teachers in favor of the post-test. There was also a statistically significant difference in critical thinking tendency scale in favor of the post-test. In the biology self-efficacy scale sub-factors of learning levels and problem-solving, there was a statistically significant difference on behalf of the post-test. However, there was not a statistically significant difference between pre-test and post-test concerning the laboratory activity sub-factor of the biology self-efficacy scale. On behalf of post-tests, there was also a statistically significant difference in critical thinking tendency scale's sub-factors as inquisitiveness, self-confidence, and systematicity. The results show that the problem-based scenario method with experiment certainly contributed to the biology self-efficacy and critical thinking tendency of pre-service science teachers. Based on these results, it is recommended that the problem-based scenario method with experiment be used in the laboratory lessons of prospective teachers.