This study sought to investigate the challenges faced in mother tongue education in selected Primary schools in Nandi County, in the Republic of Kenya. Mother tongue education is usually taken as a basic human right, but despite the importance of this education myriad of problems bedevil its execution. Challenges in mother tongue education have not only been reported in many fora in Nandi County but also elsewhere in Kenya; however, no systematic study has been carried out to document these challenges, their nature and their causes. The main objective of the study was to find out the challenges of mother tongue education in Nandi County and the possible solutions to these challenges. The study adopted a case study design against a backdrop of mother tongue theory by Butzkamm (2000) which advances the argument that mother tongue education forms the basis of a child‟s acquisition of knowledge, additional languages and self-expression. This theory is built on the foundations of arguments raised by Tangas and Toukomaa(1976) claiming that a certain threshold of first language competence is needed for second language learning. A stratified random sample of 20 Head teachers, 20 lower Primary SchoolTeachers, and 5 education officials was drawn from selected schools in Chesumei sub-County in Nandi County. The main instruments of data collection were structured and semi-structured questionnaires. Data was organized and analyzed using descriptive statistics. The study identified three major challenges facing the implementation of mother tongue education in Nandi County namely: attitude of education stakeholders; teacher related factors and lack of instructional materials. The results of this study are expected to benefit scholars in applied linguistics, ministry of education and policy makers in education.