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Abstract Background Home-based primary care (HBPC) is an emerging patient-centered, interprofessional healthcare service model that can address unmet medical needs and care burdens for homebound older adults. In December 2022, the Ministry of Health and Welfare in South Korea launched the Home-Based Medical Center Demonstration project to provide a new bundle payment for physician home visits. In this study, we seek to determine whether the recently introduced HBPC services in South Korea have been associated with a reduction in long-term care (LTC) facility admissions and acute hospitalizations among homebound older adults. Methods The study is a community-based, multicenter, two-arm, randomized encouragement design trial with a 12-month follow-up period (n = 600). Eligible study participants are community-dwelling LTC recipients with multimorbidity and functional deterioration. Study participants are recruited from five HBPC centers located in urban areas (Northeast Seoul, West Seoul, Daejeon, Wonju, and Paju). The study participants are randomly assigned to either the HBPC group or the usual care group with a 1:1 allocation ratio. Those assigned to the HBPC group receive longitudinal home visits at least once a month by an interprofessional HBPC team according to the Widely Integrated Services in Home (WISH) intervention protocol. This protocol adheres to the Integrated Care for Older People principles, which call for a person-centered assessment and broader integration of health and LTC services at the micro-, meso- and macro-levels. Primary outcomes of the trial are 1) between-group community survival days and 2) between-group potentially avoidable hospitalizations. Results of the treatment are estimated by both modified intention-to-treat and complier average causal effect analytic methods. Discussion This study aims to investigate the real-world effectiveness of HBPC on the reduction of LTC facility admissions and acute care hospitalizations in the community setting. The findings may inform healthcare policy decisions to expand HBPC services in South Korea and other countries. Trial Registration CRIS KCT0007921.