We consider the challenges and implications of controlling for school contextual bias when modeling teacher preparation program effects. Because teachers are not randomly distributed across schools, failing to account for contextual factors in achievement models could bias preparation program estimates. Including school fixed effects controls for school environment by relying on differences among student outcomes within the same schools to identify the program effects, but this specification may be unidentified. Using statewide data from Florida, we examine whether the inclusion of school fixed effects is feasible, compare the sensitivity of the estimates to assumptions underlying for fixed effects, and determine what their inclusion implies about the precision of the preparation program estimates. We discuss the implications of our results on the feasibility, precision, and ranking of programs using the school fixed effect model for policy makers designing teacher preparation program evaluation systems.