Reflux esophagitis is known to be more prevalent in males, and previous studies have suggested sex differences in its risk factors. However, little is known about sex differences in the time-course of risk factors before reflux esophagitis onset. Thus, we conducted a retrospective longitudinal study using health checkup records. From the records of 230,056 individuals obtained from nine institutes in Japan, we selected 1,558 male reflux esophagitis cases, 3,116 male controls, 508 female reflux esophagitis cases, and 1,016 female controls were selected. We compared time-courses of risk factors between the case and control groups and identified abdominal circumference (AC), diastolic blood pressure, alanine transaminase (ALT), and current smoking in males and body mass index (BMI) in females as sex-specific risk factors. We also found that AC and ALT in males and BMI in females were significantly different between the reflux esophagitis case and control groups during the five years before reflux esophagitis onset. Our results suggest that visceral fat-type obesity and fatty liver in males and higher BMI in females are more frequently observed in reflux esophagitis cases several years before reflux esophagitis onset, and that proactive intervention to lifestyle can help prevent reflux esophagitis in both males and females.