Health related quality of life (HR-QOL) of functional dyspepsia (FD) patients is impaired. However, the QOL of such patients has not been fully examined. Accordingly, we examined the QOL of Rome IV defined FD, endoscopic negative dyspeptic patients who do not meet the criteria, (non-FD patients) and healthy subjects, and investigated the factors that influence HR-QOL. This was a multicenter, prospective, observational study. Two hundred thirty-five patients (126 FD, 87 non-FD) and 111 healthy subjects were investigated, and non-FD patients were subdivided into three groups: 17 patients failing to meet only the disease duration criterion (Group A), 53 patients failing to meet only disease frequency criterion (Group B) and 17 patients failing to meet both the disease duration and frequency criteria (Group C). They completed a questionnaire survey regarding gastrointestinal symptoms (GSRS), QOL and psychological factors, which were compared among three groups. The total GSRS score was significantly higher in FD patients than non-FD patients (p = 0.012), which was higher than the healthy subjects (p < 0.0001). Furthermore, the total GSRS score of FD patients was comparable to that of Group A (p = 0.885), which was significantly higher than that of the Group B and C (p = 0.028, p = 0.014, respectively). HR-QOL is more impaired in FD patients than non-FD patients, which was significantly lower than the healthy subjects. That GSRS score in FD and Group A was comparable suggesting that an increased frequency of symptoms may have impact on the impairment of patient’s QOL.