Logic models are based on linear relationships between program resources, activities, and outcomes, and have been used widely to support both program development and evaluation. While useful in describing some programs, the linear nature of the logic model makes it difficult to capture the complex relationships within larger, multifaceted programs. Causal loop diagrams based on a systems thinking approach can better capture a multidimensional, layered program model while providing a more complete understanding of the relationship between program elements, which enables evaluators to examine influences and dependencies between and within program components. Few studies describe how to conceptualize and apply systems models for educational program evaluation. The goal of this paper is to use our NSF-funded, Interdisciplinary GK-12 project: Bringing Authentic Problem Solving in STEM to Rural Middle Schools to illustrate a systems thinking approach to model a complex educational program to aid in evaluation. GK-12 pairs eight teachers with eight STEM doctoral fellows per program year to implement curricula in middle schools. We demonstrate how systems thinking provides added value by modeling the participant groups, instruments, outcomes, and other factors in ways that enhance the interpretation of quantitative and qualitative data. Limitations of the model include added complexity. Implications include better understanding of interactions and outcomes and analyses reflecting interacting or conflicting variables.