Introduction: Critical thinking is a highly-valued skill in higher education, even though there are few studies that demonstrate its effectiveness on scientific skills of pedagogy students. The purpose of this study was to analyze the effect of a critical thinking program (PENCRIT-RC) on inquiry and probabilistic reasoning skills in pedagogy students. Method: The method was based on a quasi-experimental design, with a control group and pre- and post-test application. The participants were 95 students of science and mathematics pedagogy from two Chilean universities. The instruments used were an inquiry scale adapted from a critical thinking test, and a scale of probabilistic reasoning adapted from the Lawson classroom test. Descriptive and bivariated analisys (ancova) was applied to calculate data. Results: The results showed a statistically significant difference in both variables for the experimental group, with a large effect in the inquiry variable, and a moderate effect in the probabilistic reasoning variable. Discussion and Conclusion: It is concluded that the program is effective for the development of inquiry skills in participants, but probabilistic reasoning skills require more work in professional training.