The purpose of this study was to compare experiences of teachers and learners in the implementation of the National Strategy on Inclusive Education between primary and secondary schools in Malawi using a qualitative methodology with a phenomenological approach. The findings show that there is no clear difference in the way the National Strategy on Inclusive Education is implemented at both educational levels. Both levels face challenges of not having a system to identify and assess students for inclusive education; teachers do not have adequate knowledge and skills for inclusive education; training institutions do not offer practical programs on inclusive education; teaching and learning resources for students with special needs are not available; school infrastructure is not disability friendly; and some learners discriminate their fellow learners with special needs. These findings imply that there is a need to have all teachers trained in inclusive education; teacher training colleges and universities must offer both theoretical and practical inclusive education programs; there must be a system in schools to identify and assess learners; teaching and learning resources for those with disabilities must be provided; and conducive environment in schools that is disability friendly must be created.