For many years, educational reforms worldwide have sought to implement and improve integrated STEM education (Science, Technology, Engineering and Mathematics). This is also the case in Denmark, where integrated STEM education has gained momentum in educational policies related to primary and secondary school for at least two decades. However, there is no univocal understanding among stakeholders of what STEM is and what it entails. Even though integrated STEM approaches are an ambition for science education in Denmark, research about how successfully to implement integrated STEM education in comprehensive schools is limited. If we are to achieve more widespread implementation, it is crucial that we understand the potential barriers that impede teachers from adopting integrated STEM approaches. Based on cultural-historical activity theory, the purpose of this Ph.D. study is to explore the systemic contradictions that mediate implementation of integrated STEM education in comprehensive schools. This, in turn, can help us understand how such systemic contractions pose barriers for more widespread implementation and provide suggestions for ways of overcoming these. The Ph.D. study is based on a case study of groups of teachers from four different schools participating in the ‘Science Marathon’ program. ‘Science Marathon’ is explored as an example of integrated STEM in comprehensive schools. Data for the study was collected through participant observations and qualitative interviews and subjected to thematic analysis. Finally, selected themes were explored using an activity systems perspective on each school. The study found the following systemic contradictions across the four case schools, (1) approaching integrated STEM as science teaching or interdisciplinary teaching, (2) distinguishing between science and engineering practices, (3) teaching for science competence or content, (4) 21st century skills as relevant but vague goals, (5) inconsistency of integrated STEM object leads to varying teaching practices, and (6) integrated STEM object compatibility with local settings. These contradictions were present in each of the four schools, but they posed barriers for implementation of integrated STEM to varying degrees dependent on the local school settings. In other words, this study proposes that any attempt to implement integrated STEM needs to consider how these contradictions present themselves in local school settings.