The number of orphaned children in third world countries is on the rise. These children are facing so many challenges include lack of parental care, economic hardship in the family, stigmatization, lack of learning materials, and child labour. This results into school dropout, absenteeism, early pregnancies and marriages, immoral behavior and poor performance in their studies. But now the government has introduced free education policy thus this study intended to investigate the persisting and the new challenges facing orphaned children to access and participate in secondary school education in Nyamagana district. The study employed mixed research approach by which convergent research design was used. Also the critical theory of education was used to guide the study. The participants were; 4 heads of schools, 4 teachers dealing with orphaned children, 72 orphaned students, 8 orphaned children who are not enrolled in secondary school education, 8 guardians and 4 street leaders. Data collection was done by the use of questionnaires, interviews, document analysis and observations. Data analysis based on themes and descriptive statistics with the help of Statistical Package for Social Science (SPSS). However ethical implication was highly considered so as to meet the objectives of study. The findings of the study revealed that despite the presence of free basic education, which seems to increase the number of students from poor families, most of the teachers, guardians, street leaders and the government did not have a well-established scheme to identify and provide academic and financial support to orphaned children so that they can be able to overcome the challenges which are still there. The study suggests that all stakeholders should play their roles effectively to improve access and participation of orphaned children in secondary school education.