In an era where digital technologies are integral to daily life and sustainable education is increasingly critical, developing higher-order thinking skills with appropriate information and communication technology (ICT) support is crucial for achieving Sustainable Development Goals (SDGs). The purpose of this study was to examine synergies of systems thinking and technology-enhanced learning from the perspective of flow theory within the context of sustainable education. We surveyed more than 65 pre-service preschool teachers engaged in a design, technology, and engineering (DTE) course at the University of Ljubljana. Mapping of systems thinking revealed that pre-service preschool teachers needed support regarding feedback and understanding the interrelationship dimension of systems thinking—essential components of sustainable education. Predictive and mediation analyses yielded noteworthy results. Participants in the ICT-enhanced DTE course rated their cognitive and social engagement above the mid-point of the scale, with this higher engagement correlating with higher systems thinking crucial for sustainable education. In contrast, their aesthetic engagement was below the mid-point of the scale. Experiencing a flow state during ICT activities positively influenced systems thinking, particularly in terms of clear goals and autotelic experiences. Flow theory thus emerges as a solid and appropriate framework to use for studying synergies in technology-enhanced systems thinking for sustainable education. These findings underscore the importance of integrating systems thinking into curricula to enhance learning outcomes and prepare students for future challenges, thereby contributing to the achievement of SDGs through sustainable education.