The growing push in nonprofit studies toward panel data necessitates a methodological guide tailored for nonprofit scholars and practitioners. Panel data analysis can be a robust tool in advancing the understanding of causal and/or more nuanced inferences that many nonprofit scholars seek. This study provides a walk-through of the assumptions and common modeling approaches in panel data analysis, as well as an empirical illustration of the models using data from the nonprofit housing sector. In addition, the paper compiles applications of panel data analysis by scholars in leading nonprofit journals for further reference.