Three problems impede the assessment of hospital pharmacy efficiency. First, although multiple efficiency indicators are utilized to measure a large variety of activities, it has not been possible to validly measure overall efficiency. Second, there have been no widely-used clinical activity indicators, so key outputs often have not been accounted for. Third, there has been no effective methodology for identifying when declines in efficiency are normal random variations and when they represent true decreases in performance. This paper presents a procedure that simultaneously addresses these three problems. It analyzes data from a group of U.S. hospital pharmacies that collect an inclusive set of clinical and distributional indicators. It employs Data Envelopment Analysis to develop comprehensive efficiency measures from the numerous outputs and inputs. It applies statistical Panel Data Analysis to estimate confidence intervals within which each pharmacy’s true efficiency resides, and to develop control charts for signaling when a pharmacy’s efficiency has declined by more than can be attributed to random variation. This integrated efficiency evaluation system is transferable to other hospital pharmacy systems, thereby offering decision makers a better way of measuring, controlling and improving hospital pharmacy efficiency.