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Teaching the complexity of educational systems is challenging and can produce oversimplified representations. Students struggle to connect macro-level systemic processes to individual psychological experiences within educational systems, and, more generally, to undergo the conceptual changes required to understand educational systems as complex systems (with non-linear interactions and emergent causalities). We present the preliminary implementation and results of a pilot course for undergraduate psychology and educational sciences students that integrates agent-based modeling with conceptual change research to teach educational systems as complex systems. The visualisation and in-silico experimentation capabilities of agent-based modelling create a structured prediction-verification-explanation cycle that leverages students’ prior knowledge by promoting conceptual change. This approach offers promising directions for making complex systems thinking accessible to social science students.