Amid demographic and social changes in contemporary Japan, the growing prevalence of loneliness and social isolation has emerged as a critical societal issue. This comprehensive review examined domestic research trends in Japan and addressed the definitions, underlying mechanisms, and measurement challenges of these concepts. By using structural topic modeling with the J-STAGE database, this article analyzed cross-disciplinary domestic research trends on loneliness and social isolation over time, revealing the significant expansion of the field since the 2000s—particularly in psychology and medicine. Theoretical frameworks underlying the concepts of loneliness, social isolation, ostracism, and social exclusion are introduced, with particular attention to the implications of interpersonal relationships on health, including stress-buffering and main effect models, and developmental and evolutionary perspectives on loneliness. This review also critically evaluated methodological issues, including the classical statistical problem of dichotomizing continuous variables and the challenges in categorizing individuals by using arbitrary thresholds in loneliness and social isolation scales. In conclusion, meaningful progress in the field requires a thorough understanding of theoretical foundations, as well as methodological considerations in measuring loneliness and social isolation.