The study aimed to analyze the factors influencing the implementation of systems thinking in the Physical Education and Health Department of the Ministry of Education, with a focus on enhancing the effectiveness of educational and sports organizations. This applied research was conducted using an exploratory mixed-methods approach (qualitative-quantitative). The qualitative phase included experts in the fields of physical education and health within the Ministry of Education, as well as university professors, selected through purposive sampling. The quantitative phase involved all specialists working in the Physical Education and Health Departments across the country (236 individuals), and given the limited population, a census approach was applied. In the qualitative phase, semi-structured in-depth interviews were used, while in the quantitative phase, a researcher-developed systems thinking questionnaire and an organizational effectiveness questionnaire were employed to collect data. Data analysis was conducted using thematic analysis for the qualitative phase, and Kolmogorov-Smirnov test, Friedman test, and partial least squares (PLS) method for the quantitative phase. The qualitative findings indicated that the identified factors influencing systems thinking comprise four overarching categories: individual-personal factors, organizational factors, contextual (environmental) factors, and extra-organizational factors. Moreover, the prioritization of these factors revealed that organizational factors ranked first, individual-personal factors second, extra-organizational factors third, and contextual factors fourth. The path coefficient between systems thinking and organizational effectiveness was 0.657, with a t-value of 14.456, indicating a significant and direct relationship. Based on the findings, strengthening systems thinking among specialists and managers in the physical education and health sector can improve organizational effectiveness within the Ministry of Education. Therefore, it is recommended that policymakers and managers in this field focus on enhancing organizational structures, fostering a culture of collaboration and organizational learning, and providing training programs grounded in a systems thinking approach to promote efficiency and cross-functional coordination.