Research has indicated that the effectiveness of school-based prevention programs is affected by the implementation quality of these programs. As the importance of implementation has become clear, researchers have identified factors that appear to be related to implementation quality, including local program selection and training, integration into school operations, organizational capacity, principal support, and program standardization; however, it is unknown whether the impact of these factors differs by program type. Data from a nationally representative sample of 544 schools are used to create structural equation models representing hypothesized relationships among school and program factors and implementation quality, controlling for exogenous community factors. The relative importance of these factors for individual-level programs, such as behavior modification and counseling programs, versus environmental-level programs, such as improvements to classroom management or school planning and climate change programs, is the focus of this study. Implications for the implementation of school-based prevention program are discussed.