Yonaguni Island is a remote and isolated westernmost island in Japan, which is the fastest aging country in the world. This study evaluated the current status of medical supply-and-demand on the island and compared these results with previous surveys carried out in rural parts of Japan. This was a retrospective cohort study conducted at the Yonaguni Municipal Clinic, the only medical facility in Yonaguni Island. The participants were patients who visited the clinic over one year, between July 2015 and June 2016. We calculated the rate per 1,000 persons per month of clinic visits, referrals to off-island medical facilities (e.g., hospitals and specialist clinics), referrals to off-island emergency departments, off-island hospitalizations after referral, home visits, and overnight observations at the clinic. In total, 6,197 patients (males, 46.3%) visited the clinic. The rate of clinic visits per 1,000 persons per month was 516.4 (Standard deviation [SD] 28.1, 95% confidence interval [CI]: 500.5–532.3). The rate per 1,000 persons per month was 14.0 (SD 3.9, 95% CI: 11.8–16.2) for off-island referrals, 3.8 (SD 2.1, 95% CI: 2.6–5.0) for referrals to emergency departments, 4.8 (SD 2.6, 95% CI: 3.3–6.2) for hospitalizations, and 3.2 (SD 1.7, 95% CI: 2.2–4.1) for home visits. The rate of clinic visits was higher in Yonaguni Island than in other rural areas, although the rate of off-island referrals was lower. There were no significant differences between the number of referrals to emergency departments, hospitalizations, and home visits in Yonaguni Island, in comparison to other studies. Our study showed that patients presenting with emergencies had similar rates of healthcare-seeking behavior to those reported in previous studies in Japan; however, the referral rate was lower. We assessed the ecology of medical care in this district by evaluating patient behavior on an isolated island where access to medical care is geographically limited.