Background: Many U.S. health care institutions have adopted compensation models based on work relative value units (wRVUs) to standardize payments and incentivize providers. A major determinant of payment and wRVU assignments is operative time. We sought to determine whether differences in estimated operative times between the Centers for Medicare & Medicaid Services (CMS) and the National Surgical Quality Improvement Program (NSQIP) contribute to payment and wRVU misvaluation for the most common shoulder/elbow procedures. Methods: We collected data on wRVUs, payments, and operative times from CMS for 29 types of isolated arthroscopic and open shoulder/elbow procedures. Using regression analysis, we compared relationships between these variables, in addition to median operative times reported by NSQIP (2013–2016). We then determined the relative valuation of each procedure based on operative time. Results: Seventy-nine percent of CMS operative time were longer than NSQIP time (R2 = 0.58), including, but not limited to, shoulder arthroplasty and arthroscopic shoulder surgery. The correlation between payments and operative times was stronger between CMS data (R2 = 0.61) than NSQIP data (R2 = 0.43). Similarly, the correlation between wRVUs and operative times was stronger when using CMS data (R2 = 0.87) than NSQIP data (R2 = 0.69). Nearly all arthroscopic shoulder procedures (aside from synovectomy, debridement, and decompression) were highly valued according to both datasets. Per NSQIP, compensation for revision total shoulder arthroplasty ($10.14/min; 0.26 wRVU/min) was higher than that for primary cases ($9.85, 0.23 wRVU/min) and nearly twice the CMS rate for revision cases ($5.84/min; 0.13 wRVU/min). Conclusions CMS may overestimate operative times compared to actual operative times as recorded by NSQIP. Shorter operative times may render certain procedures more highly valued than others. Case examples show that this can potentially affect patient care and incentivize higher compensating procedures per operative time when less-involved, shorter operations have similar patient-reported outcomes.