Background: The crucial role of adequate water, sanitation and hygiene (WASH) facilities in influencing children's handwashing behaviour is widely reported. Report from UNICEF indicates a dearth of adequate data on WASH facilities in schools, especially in the developing world. This study sought to contribute to building the evidence-base on school hygiene facilities in Ghana. The study further explored for possible associations and differences between key variables within the context of school water, sanitation and hygiene. Methods: Data was collected from 37 junior high schools using an observational checklist. Methods of data analysis included a Scalogram model, Fisher's exact test, and a Student's t-test. Results: Results of the study showed a facility deficiency in many schools: 33% of schools had students washing their hands in a shared receptacle (bowl), 24% had students using a single cotton towel to dry hands after handwashing, and only 16% of schools had a functional water facility. Furthermore, results of a proportion test indicated that 83% of schools which had functional water facilities also had functional handwashing stations. On the other hand, only 3% of schools which had functional water facilities also had a functional handwashing stations. A test of difference in the proportions of the two sets of schools showed a statistically significant difference (p < 0.001). In addition, 40% of schools which had financial provisions for water supply also had functional handwashing stations. On the other hand, only 7% of schools which had financial provisions for water supply also had functional handwashing stations. There was a statistically significant difference in the proportions of the two sets of schools (p = 0.02). Conclusion: We conclude that it is essential to have a financial provision for water supply in schools as this can potentially influence the existence of a handwashing station in a school. An intervention by government, educational authorities and civil society organisations towards enabling schools in low resource areas to have a sustainable budgetary allocation for WASH facilities would be timely.