This manuscript is the product of the authors’ discussions, literature overview, and consultation with experts in the field, and identifies important gaps in the evidence base for substance use disorder (SUD) treatment effectiveness within criminal justice (CJ) settings. Lacking from the extant literature are longitudinal investigations of treatment related outcomes during and after incarceration. Such studies could provide rich contextual data about treatment delivery and effectiveness across the CJ continuum, and would provide important insight into individual characteristics (e.g., motivation, treatment modality preferences, treatment completion rates, etc.) as well as institutional and environmental factors (e.g., appropriate staffing, space limitations for individual treatment sessions, distribution of medications, etc.). We also identified the importance of reproducibility within CJ research, and the unfortunate reality of too many single studies conducted in single (or relatively few) correctional facilities. Some of this has been because the studies designed to produce that evidence are not prioritized for funding, which has continually placed researchers in a position where we cannot make firm conclusions or recommendations based on available evidence. The importance of replicating the foundational studies in this field cannot be overstated. We hope this article spurs other researchers to join in the healthy process of questioning the existing state of the CJ-based SUD treatment research, what should be re-examined, and how we can lay a stronger foundation for the future.