The purpose of this paper is to examine the challenges of school-based counselling and its future direction in Nigeria. In this endeavour, the author discusses the following possible challenges militating against the smooth running of effective school-based counselling services to include inadequate counselling materials and work tools, deployment of school counsellors to perform non-counselling duties, insufficient training of professional counsellors, lack of clarification of the role of school counsellors, school principals' low collaboration with school counsellors amongst others. The paper also focused on ways and means of improving school-based counselling services to include enactment of proper policy intervention, putting in place a functional school inspectorate division, improving counselling facilities and equipment in schools, encouragement of regular counsellors' attendance at workshops, seminars and conferences (i.e., training and retraining of school counsellors) for self-capacity building amongst others.