The five-dimension service quality (SERVQUAL) scale is one of the most common tools for evaluating gaps between clients’ perceptions and expectations. This study aimed to assess the quality of health services in Iran through a meta-analysis of all Iranian studies which used the SERVQUAL tool. A systematic literature review has been performed in Web of Science, PubMed, Scopus, Google Scholar, Iran Medex, Magiran and Scientific Information Database. All relevant English or Persian studies published between January 2009 and April 2016 were have been selected. Papers were considered if they regarded all five dimensions of the SERVQUAL tool for assessing the quality of health care services. Two reviewer independently extracted mean and standard deviation of five dimensions and characteristics of studies. The quality of studies included in meta-analysis using STROBE checklist. Of 315 studies initially identified, 12 were included in our meta-analysis. All analyses were performed in Stata MP v. 14. Patients’ perceptions were lower than their expectations (gap = −1.64). Responsibility (−1.22) and reliability (−1.15) had the lowest gaps, and tangibility and empathy (−1.03) had the largest gaps. Except gender, other variables had no significant associations with gaps. Patients in the cities of Arak (−3.47) and Shiraz (−3.02) had the largest gaps. All dimensions of service quality were negative, which implies that the quality of health services in Iran has not been satisfying to patients and needs to be improved.