Background: Separation anxiety disorder (SAD) is one of the most common disorders among children's behavioral problems, which leads to disruption in academic performance, social adjustment, family life, and peer relationships. Cognitive-behavioral play therapy (CBPT) is one of the appropriate treatment methods for correcting children's behavioral problems. It is designed for children aged three to eight. Objectives: Considering the importance of controlling separation anxiety in primary school children, the main aim of this research was to assess the effectiveness of CBPT in reducing SAD in boys in the first grade of primary education. Methods: A total of 30 primary school students with SAD were selected and then divided into the experimental group (15 students) and the control group (15 students) to conduct the present study. For the control group, no intervention was performed, but CBPT was done in ten sessions for the experimental group. The level of SAD was evaluated in both groups and then compared with each other before and after the intervention. In addition, the level of SAD in both groups was compared between the pre- and post-study stages to assess the effect of CBPT. The statistical analysis of the results was performed using SPSS software version 24 and using relevant tests at the significance level (α = 0.05). Results: The results showed that the average SAD score before the intervention was equal to 78.84 ± 1.26 for the control group and 78.66 ± 1.28 for the CBPT group. The statistical analysis revealed no significant distinction across these average levels (P = 0.975). After the intervention, the average SAD for the control and experimental groups was 77.50 ± 1.65 and 47.75±0.76, respectively, showing a significant difference between the two values (P < 0.001). Conclusions: Based on the findings, CBPT can reduce SAD in primary school children. Therefore, psychologists and educational counselors of elementary school students can recommend using CBPT to treat some behavioral problems of elementary students.