The purpose of this study was to quantify how school sanitation conditions are associated with pupils' use of sanitation facilities. We conducted a longitudinal assessment in 60 primary schools in Nyanza Province, Kenya, using structured observations to measure facility conditions and pupils' use at specific facilities. We used multivariable mixed regression models to characterize how pupil to toilet ratio was associated with toilet use at the school-level and also how facility conditions were associated with pupils' use at specific facilities. We found a piecewise linear relationship between decreasing pupil to toilet ratio and increasing pupil toilet use (p < 0.01). Our data also revealed significant associations between toilet use and newer facility age (p < 0.01), facility type (p < 0.01), and the number of toilets in a facility (p < 0.01). We found some evidence suggesting facility dirtiness may deter girls from use (p = 0.06), but not boys (p = 0.98). Our study is the first to rigorously quantify many of these relationships, and provides insight into the complexity of factors affecting pupil toilet use patterns, potentially leading to a better allocation of resources for school sanitation, and to improved health and educational outcomes for children.