PurposeEducation for sustainable development (ESD) has gained significant attention, but integrating ESD into existing education systems is challenging. The study aims to explore the challenges of ESD experienced by school leaders, focusing on the context of Malaysian schools.Design/methodology/approachThe study uses a qualitative approach with a single-case study design. Eight school leaders involved in the Johor sustainable education action plan (JSEAP) were interviewed and analyzed. The study uses thematic analysis to identify the challenges and other causes associated with the implementation of ESD.FindingsThis study revealed that the school leaders perceived the ESD challenges at three levels. First, restriction to the standardized curriculum (systemic); second, resistance to change (organization) and third, awareness and readiness (individual). These themes stemmed from seven primary codes that school leaders encountered throughout the JSEAP program.Research limitations/implicationsThis paper is limited to a case study of the chosen schools and cannot be extrapolated to a larger population.Practical implicationsThe study benefits school leaders and educators concerned about ESD and its role in their schools and other academics interested in ESD.Originality/valueTo the authors' knowledge, this is the first study to investigate ESD challenges in Malaysia. The novel discovery of the three levels of ESD challenges helps readers better understand the recent phenomenon of ESD implementation and compare it to other settings.