This study examined the factors influencing the choice of Health Education as West African Examination Council (WAEC) subject at senior secondary school certificate examination among secondary school students in Ago-Iwoye Township. A purposive sampling technique was used to select sixty (60) Senior Secondary School students who registered for Health Education. A questionnaire designed and validated by the researcher was used to gather relevant information. Data collected were analysed with the use of chi-square test. Findings revealed that personal interest, availability of health facilities, availability of equipment, parents and peers will significantly influence the choice of Health Education at West African Examination Council among Secondary School students in Ago-Iwoye Township. Based on this findings, it was recommended that students’ personal interest should be greatly considered in the choice of Health Education subject and the school counsellors should be more enlightened on the relevance of Health Education to the national development.