Background: Complexity theory (CT) has been used in response to the need for a different mindset than the classical engineering paradigm. The engineering education research (EER) community may benefit from the knowledge of how CT has been used in the field. Purpose: Aiming to provide a broad view of CT in EER, the following research questions guided the study: How has CT been applied in EER, and how does it contribute to addressing the challenges of classical engineering education? What are the different complexity engineering approaches, and how can they be integrated into the context of EER? Method: A systematic literature review was conducted. The review process was divided into three stages: planning, conducting, and reporting. Fifty-eight journal articles and five book chapters were submitted to an iterative process of organization, categorization, analysis, and synthesis. Results: Complexity schools of thought were integrated into EER. The research was organized into thematic categories: epistemological and ontological perspectives; complex thinking and competences; pedagogical approaches; complexity, sustainability, and transdisciplinarity interdependence; engineering axiology; and systemic transformation of engineering education. For each category, main contributions were integrated, and gaps were identified. Different meanings of complexity engineering were discussed and related to complexity schools of thought. Conclusions: Defining the type of complexity approach used is essential to advance knowledge, as there are fundamental epistemological, ontological, and methodological differences. Thematic categories help future researchers position theoretical contributions and be precise about how their findings contribute to understanding complexity applications in EER. Overcoming the limits of classical engineering requires a paradigmatic discussion, and CT proves valuable for this.