Background: Attention to children's nutrition is important; since they are the most sensitive and vulnerable group in the community against malnutrition and food shortages. Therefore, this study aims to design, implement, and evaluate the effect of educational programs based on (philosophy for children) on thinking skills about healthy breakfast consumption of sixth-grade elementary school students in Yazd. Methods: The present clinical trial study was performed on 120 sixth-grade students of public schools in Yazd. Data were collected using a researcher-made questionnaire in control and experimental groups before and after the educational program. Results: The results showed that the mean score of critical thinking after the intervention (38.7 ± 81.1) in the experimental group (EG) increased compared to before the intervention (29.2 ± 96.4), which was statistically significant (P < 0.001). Based on the results, the difference observed in the mean score of critical thinking, caring, and creative thinking of sixth-grade students before and after the intervention in the two groups was significant (P < 0.001). On the other hand, the mean score of students' critical, caring, and creative thinking in the EG increased. In other words, the designed educational program improved all three skills in the EG. The mean scores of critical, caring, and creative thinking of sixth-grade students in the control group (CG) before and after the educational program in two stages were not significant (P > 0.05). Conclusion: According to the obtained results, the implementation of philosophy education programs for children raises the level of critical thinking, caring, and creative skills in students to eat a healthy breakfast. Therefore, increasing philosophical thinking in students and improving the studied skills through education, even virtually, can be very valuable and effective.