JVC-001 is a novel measles-mumps-rubella (MMR) combined vaccine. In the J301 clinical trial, healthy 1-y-old Japanese children received either JVC-001 or marketed measles-rubella (MR) and mumps vaccines as control group. Our aim was to compare the long-term results between these two groups. From the 861 participants in the J301 study, 502 were followed for approximately 4 y. Antibody titers were measured using measles neutralizing test (NT), rubella hemagglutination inhibition (HI), mumps plaque reduction NT (PRNT) against genotype D and NT against genotype G in total of 446 participants (216 in the JVC-001 group, 230 in the control group). No participants in either group were identified as having measles, rubella, or mumps during the study period. Seropositive rates of measles NT, rubella HI, mumps PRNT (genotype D) and mumps NT (genotype G) in the JVC-001 group were 93.5%, 98.6%, 91.7%, and 88.9%, respectively. The control group rates were 88.7%, 99.1%, 92.4%, and 87.4%, respectively. JVC-001 maintained antibodies against measles, rubella, and mumps for approximately 4 y, with comparable persistence to marketed vaccines. The results suggested that protective serum antibodies are maintained until the second dose of MMR vaccine is administered in a Japanese pediatric population. Trial registration: jRCTs031230590.