Learners have a right to education regardless of their limitations. However, there are still schools that are struggling to address learning barriers. This paper explores the impact of learning barriers on academic performance in selected secondary schools in Mtata, South Africa. The study was guided by the Ecological System and Inclusion Theories. A qualitative approach and case study design was adopted. Convenient and purposive sampling techniques were used to select 3 schools and 18 participants respectively. Data were gathered through semi-structured interviews. Thematic frames and thick descriptions were used to analyze data. Findings indicate that learners with learning barriers such as disabilities faced myriad of challenges including lack of resources, inability to attend to learners with challenges due to overcrowded classes and inadequate inclusive education training. The paper concludes that learning barriers have a negative bearing on the academic performance of learners. Effective inclusive education policies, teachers’ training, parental involvement and psychological support for learners are a necessity. Regardless of challenges, some teachers are scaffolding these learners. For improvement on learners’ academic performance, there is need for collaboration of government, parents and teachers. The use of technology in South African rural schools should be a priority. Providing learners with digital tools and skills to facilitate learning is important as technology in the classroom will facilitate teaching methodology variation and management of overcrowded classes. Future study should focus on the impact of using digital tools on the academic performance of learners with learning barriers.