As the healthcare system shifts from fee-for service toward value-driven healthcare, interest has grown in medication-related quality metrics to evaluate quality and value within the healthcare system. While the Defense Health Agency (DHA) has taken steps to align healthcare quality measures across the enterprise, the extent to which DHA utilizes pharmacy quality measures (PQMs) or evaluates the quality of direct and purchased pharmacy care is unknown. A comparison was made between existing PQMs utilized by DHA and all measures published and endorsed by the Pharmacy Quality Alliance (PQA), a recognized, PQM standard-setting organization. We also compared DHA PQMs to those used within the Medicare Part D Star Rating Program. DHA has implemented 10 (28%) of the 36 PQA measures available for evaluation as of August 2019. Of the five measures included in the 2020 CMS Part D Star Rating program, DHA has currently implemented four (80%) of the measures. DHA has implemented 3 of the 5 (60%) PQA CMS Display Measures, and 5 of 9 (56%) PQA CMS Patient Safety Report Measures that are not part of the Star Ratings, but that are used to benchmark and provide feedback to health plans. Opportunities exist within the DHA to leverage PQMs to evaluate the quality of pharmaceutical care, build trust with beneficiaries by increasing transparency, and maintain parity with the civilian healthcare system. Existing models and commercially available technology could be considered to rapidly operationalize the use of PQMs within the MHS.