Teenage pregnancy leads to dropout of girls from school. As a consequence, it makes the girl child incapable of fending for herself and to become socially and economically unproductive in society. In Nyamira South Sub-County, the number of teenage pregnancies is on the increase despite the various government interventions to mitigate the vice and enable teenage mothers continue with their studies. Such interventions include the government policy of integration of the teen mothers in school which was introduced in 1994. The policy allows teen mothers to come back to school to continue with their studies after delivery. However, little is known in the international literature on the challenges teen mothers who come back to school after delivery to complete their studies face and to what extent they are taking advantage of the integration policy. The purpose of this study was to establish the challenges facing teen mothers’ integration in mixed secondary schools in Nyamira South Sub-County of Nyamira County, Kenya. The specific objectives of the study were to establish the academic and socio-economic challenges teen mothers face in mixed schools and to establish measures that can curb teenage pregnancies in schools in Nyamira South Sub-County. Descriptive survey design was employed in the study. The study population comprised 42 principals, 42 guidance and counseling teachers and 5953 girls. Clustered sampling was used to select 13 public mixed secondary schools in the Sub-County whose principals, guidance and counseling teachers and students participated in the study. Questionnaires and interview schedules were used to collect data. Face validity of the instruments was determined by three experts from the faculty of Education, Kisii University, who ensured they complied with universal standards of proposal and research finding reporting. Data collected was summarized and analyzed quantitatively and qualitatively. The study revealed that teenage mothers in school were stigmatized, discriminated and experience financial challenges that make them drop out of school. The study concluded that the challenges teenage mothers face in school need urgent remedy for Kenya to realize the Sustainable Development Goals (SDGs) and Vision 2030. The study recommended further research on challenges facing teenage mothers’ integration in pure girls’ boarding schools and in primary schools.