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 stu-dents. 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 ex-perimental 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 develop-ment of inquiry skills in participants, but probabilistic reasoning skills require more work in professional training