The implementation of the National Special Needs Education Policy Guidelines in Malawi began in 2009. There is limited literature on how the guidelines are implemented in secondary schools, particularly in private secondary schools of Malawi. Therefore, the study aimed at exploring the implementation of the guidelines in private secondary schools. The study used a phenomenological design and qualitative methodology. Data were generated through a triangulation of methods including semi-structured interviews, observation and document analysis. The data generated were analysed thematically. The findings revealed that there was a lack of thorough knowledge of the guidelines, resources for implementing the guidelines in private secondary schools were not available, and support for learners with special education needs was not sufficient. The results of this study indicate that communication with key school stakeholders is key for the effective implementation of the National Special Needs Education Policy Guidelines.