Although Philadelphia’s nineteenth-century public school system was praised by some contemporaries for its efficient administration, the city’s sudden embrace of clinical discourse and “bottom-up” hygienic initiatives between 1896 and 1898, along with critical reports on poor sanitary conditions by the early 1910s, suggest underlying structural issues. This paper contributes to the material history of education by examining the organizational context of Philadelphia’s school construction efforts, focusing on overcrowding and ventilation problems. Drawing from statistical data, works on school architecture, and a sample of representative school buildings, I argue that the city’s legacy of early Lancasterian designs, inconsistent architectural standards, decentralized school construction, and conflicts between local and central authorities hindered compliance with sanitary standards, compromising the health of teachers and pupils. Philadelphia’s lag in sanitary provisions in comparison to other US cities underscores the material consequences of these conflicts, shedding light on the city’s late-1890s push for clinics and dispensaries.