Skill-based Health Education is an approach to Health Education that is effective, interactive, engaging and meaningful. It focuses on skills and functional knowledge of health issues within a society. The importance of Health Education cannot be overemphasized as it plays significant role in preventing disease, prolonging life and protecting health. The extent to which the objectives of school Health Education can be realized is closely tied to assessment procedures that will be effective in assessing the skills taught. This is because a critical role assessment plays is to serve as a tool to support instructional processes. In a century characterized by explosion of knowledge as well as emerging challenges, skill-based Health Education has evolved as a responsive tool to surmounting the myriads of health challenges in this century. There is therefore an overwhelming need for a paradigm shift in the assessment procedures of school Health Education to critically evaluate the ability of learners to apply the skills in addressing contemporary societal health challenges. This paper attempts to propose appropriate assessment procedures for skill-based Health Education in Nigerian schools.