Purpose This study explored young female adolescents’ understanding of pubertal body changes and knowledge of their reproductive system. Method Female students in grades seven, eight and nine were recruited from eight junior high schools in Kupang. Body mapping was conducted together with a semi-structured interview. Data was analysed using inductive thematic analysis. Result Participants listed their pubertal body changes and then located the female reproductive system on body maps. Participants aware the changes in their five body areas and could name one or two organs in the female reproductive system but they were unable to locate them on the body maps. Conclusion The study identified a gap in young female adolescents’ knowledge about the anatomy and physiology of the female reproductive system. This study provides evidence on the value of using the body mapping exercise in conjunction with semi-structured interviews in research with young female adolescents on a sensitive topic.