HIV/AIDS is one of the most important public health challenges facing Nigeria today. Recent evidence has revealed that the adolescent population make up a large proportion of the 3.7% reported prevalence rate among Nigerians aged 15-49 years. School-based sexual health education has therefore become an important tool towards fighting this problem. This systematic review assesses the efficacy of these educational programmes and examines how future programmes and their evaluations can improve. Primary literature published between January 2002 and May 2012, which measured sexual health outcomes among school-based Nigerians before and after a sexual health education programme was delivered, was identified. All seven studies that met the inclusion and exclusion criteria showed there had been positive changes in outcomes following these educational programmes. These included increased knowledge, healthier attitudes and safer sexual health behaviour. However, these studies each had methodological flaws which highlighted a range of important design, implementation and evaluation challenges that future programmes need to meet.