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Objectives The importance of school water, sanitation, and hygiene (WASH) in achieving the Sustainable Development Goal targets 6.1 and 6.2 in developing countries cannot be overemphasized. However, widespread WASH inequalities remain an impediment to achieving the targets by 2030. Hence, this study was conducted to examine current school-WASH disparities among public and private schools in a low-income Nigerian community using mixed methods. Methods The cross-sectional survey utilized multi-stage sampling to select 400 students from five public and five private schools in Akinyele, Ibadan. Semi-structured questionnaires and observational checklists were used to obtain data. Inferential statistics were measured at a 95% confidence interval. Independent variables like the students’ sociodemographic characteristics, school type, and available WASH facilities were associated with dependent variables like respondents’ hand hygiene and sanitation practices and WASH-associated knowledge and attitude to examine existing inequalities. Results Classifying the available WASH facilities based on the WHO/UNICEF Joint Monitoring Programme, none of the public schools provided any sanitation and hygiene service, while all the private schools provided both services. Furthermore, the private-school students had significantly better WASH knowledge ( p &lt;0.001;  Ƞ  2  p =0.152) and attitude ( p &lt;0.001;  Ƞ  2  p =0.036) compared with the public-school students. Also, a significantly higher portion of public-school students practiced open defecation at school ( p &lt;0.001; odds ratio (OR)=7.4; confidence interval (CI)=4.1–13.5) and at home ( p &lt;0.001; OR=7.8; CI=3.7–16.7). Conclusion WASH disparities among socioeconomic groups remain a persistent challenge. Sole reliance on the Government to narrow the inequalities has persistently proven unfruitful. There is a need to empower local community stakeholders to facilitate sustainable school-WASH interventions.

School water, sanitation, and hygiene inequalities: a bane of sustainable development goal six in Nigeria