This study assessed the knowledge and perception of the role of water supply, sanitation and hygiene (WASH) in the containment of Ebola virus disease (EVD) among secondary school students in Ibadan, Nigeria. A cross-sectional study of 420 students from eight schools (public and private) in Ibadan was conducted. A semi-structured questionnaire and an observational checklist were used to collect data. Data were analysed using descriptive statistics, Chi-square test and logistic regression at 5% level of significance. Overall, 60% reported EVD was airborne. A majority (71%) of the respondents had good knowledge of EVD, while a majority (92%) had a good perception of the role of WASH in EVD containment. Class of respondents was significantly (p = 0.045) associated with knowledge of WASH. Although schools had satisfactory sanitary facilities, only a few (21%) sustained good hygiene practices at the end of the Ebola outbreak in Nigeria. Our findings revealed suboptimal knowledge on transmission of EVD, and unsustainable hygiene practices among secondary students post-Nigeria's EVD outbreak. High priority should be given to hygiene education among educators and students. Implementation of monitoring and evaluation of hygiene behaviour among secondary school students should also be a priority.