Personal relative deprivation (PRD) refers to emotions of resentment and dissatisfaction caused by feeling deprived of a deserved outcome compared to some referent. While evidence suggests that relative deprivation based on objective data such as income affects well-being, subjective PRD has been less explored, especially in the East. This study evaluated the relationship between PRD and subjective well-being based on various aspects in the context of Japan. An online questionnaire survey, including the Japanese version of the Personal Relative Deprivation Scale (J-PRDS5) and various well-being indices, was administered to 500 adult participants, balanced for sex and age. Quantitative data analysis methods were used. PRD significantly correlated with subjective well-being as assessed by various aspects. Through mediation analysis, we found that a strong tendency to compare one's abilities with others may undermine subjective well-being through PRD. The results also indicated that well-developed human environments may be associated with the maintenance of subjective well-being levels, even when PRD is high. Toward developing future interventions to improve well-being and health, efforts must be undertaken in Japan to monitor PRD and further clarify the mechanism of the association between PRD and the factors that showed a strong relationship in this study.