Incorporating scientific and critical thinking in early childhood education is essential for developing individuals with strong thinking skills. This study assesses the impact of promoting scientific thinking on the development of critical thinking among fifth-graders in central Mexico. We hypothesize that involving students in scientific thinking tasks would further enhance essential thinking skills. The methodology involved longitudinal quasi-experimental design that included a pre-test and post-test, along with a comparison (control) group. Critical thinking was measured using a test that was applied at the start and end of our study to assess four thinking skills: classification, problem-solving, decision-making and logical reasoning. The control group was taught using a standardized methodology, while the experimental group was taught about the structure of the scientific method using a template with characters that guided each step: observation, question, hypothesis, experimentation and conclusions. Students from the critical and scientific thinking experimental group had higher scores on the post-assessment than those of the control group, suggesting that learning through scientific thinking tasks improved their critical thinking skills. Boys’ critical thinking scores were higher than girls’ in both groups, while scientific thinking scores were not associated with gender. We demonstrated that critical thinking improves when children incorporate scientific thinking into their learning abilities.