Background: While researchers have demonstrated the positive effects of School-Based Health Centers (SBHCs) on student health outcomes, less is known about the long-term impact of SBHC use on academic outcomes, such as attendance. Objective: Our objective was to examine the direct and indirect effects of SBHC use on attendance among high school students over time. We posed three hypotheses: (1) SBHC use will predict less absenteeism, (2) SBHC use will positively predict physical activity and health status, and (3) The relationship between high school students' SBHC use and absenteeism will be mediated by physical activity and health status over time. Method: Using structural equation techniques, we estimated autoregressive cross-lagged models for a subsample of high schoolers (N = 413) from a 3-year statewide SBHC evaluation. Results: SBHC use did not predict self-reported health status, physical activity, or attendance, but was predicted by physical activity and absenteeism. In addition, student health status, physical activity, and attendance were positively correlated with each other cross-sectionally and longitudinally. Conclusions: Our findings build upon previous research on the important role student health plays in attendance and provide unique insights into the potential bi-directional relationship between student SBHC use and attendance, suggesting that SBHCs could be an opportunity to connect students to non-healthcare resources. Several implications also emerged for future longitudinal SBHC research, such as more frequent data collection intervals and examining the effects of different types of SBHC use with clinic or electronic health record data.