The primary objective of this paper was to determine the factors that affects health instruction in secondary schools in Edo State, Nigeria. The descriptive survey research method was used for the study and data were analyzed descriptively using frequency count and percentages. The results of the study reveals that school principals negative administrative styles and the inadequacy of duration/time allotted to health instruction in the schools were critical factors that affects health instruction in Edo State secondary schools. The study equally show that lack of health education teachers, lack of relevant health education textbooks, pamphlets and posters were factors central to the poor state of health instruction in Edo State secondary schools. Based on the findings, the authors made several recommendations including the need for school authorities in Edo State to provide relevant and modern textbooks, pamphlets, posters, computers and other related instructional materials. It was also recommended that the State’s Ministry of Education should help in enhancing the tenets of health education by posting at least one experienced health education staff in the Inspectorate Division of the Ministry had been assigned the responsibility of visiting the schools regularly in order to ensure that the schools, students and teachers are adequately implementing the health education curriculum.