Background: Medicare uses a quality incentive program (QIP) criteria to evaluate care in dialysis facilities and apply monetary penalties on underperforming facilities. Smaller dialysis facilities are likely to be rural and operate on lower profit margin; therefore, such facilities are likely to underperform and face Medicare penalties. The variation in QIP scores by facility size is not yet known. We investigated the association between freestanding dialysis facility size and QIP scores. Methods: Our cross-sectional analysis compared QIP scores across levels of facility size for 5,193 freestanding dialysis facilities that received QIP scores in 2015. We used Medicare facility data including Dialysis Facility Compare, Performance Scores, Facility-Level Impact, and Area Health Resource and United States Renal Data System files for the payment year 2015. We measured the facility size using the number of dialysis stations per dialysis facility. QIP scores were used to determine the quality of care. A generalized linear model was estimated at an alpha level of 0.05. Results: Facilities operating more than 10 dialysis stations scored higher than those operating fewer. Further, facilities in the South and Northeast, not offering peritoneal dialysis, affiliated with chains (except chain 3) and spending more hours per dialysis achieved higher QIP scores. Facilities reporting a higher proportion of Hispanic patients and of patients with access to pre-end-stage renal disease (ESRD) nephrologist care achieved higher QIP scores. Conversely, facilities with a higher Black patient population and higher patient travel distances scored lower. Conclusions: The current study provides important finding about the performance of the dialysis facilities with ≤10 dialysis stations. Quality improvement strategies are needed, especially for the dialysis facilities with ≤10 stations, to prevent penalties and eventual closure of such facilities due to financial insolvency. Failure to address these issues will increase further disparities in ESRD care.