This cross-sectional study investigated the association between eating alone at each meal and health status, including functional capacity among community-dwelling Japanese elderly living with others. A self-administered questionnaire was mailed to all 8004 residents aged 65 or older, residing in the same Japanese town in March 2016. Eating alone was assessed by first asking whether participants ate three separate meals each day (i.e., breakfast, lunch, and dinner), and those who answered affirmatively were then asked how many people were usually present at each meal. Health status was assessed in terms of subjective health, medical history, care needs, body mass index, depression, and functional capacity. Data from 2809 respondents were analyzed. Those who reported not being in good subjective health and a history of hypertension were significantly more likely to eat alone at breakfast (odds ratio 1.27; 95% confidence interval 1.01-1.61, and 1.26; 1.06-1.49). Depressive symptoms and many subscales of functional capacity were also significantly associated with eating alone at breakfast, lunch, and dinner (p < 0.05). Many health status indicators were related to eating alone at each meal, especially breakfast.