This study evaluated the effects of vaccination for Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni in young Japanese Black calves at an ordinal farm, where respiratory diseases frequently occur at a young age. In total, 105 calves were divided into the vaccination group (n = 52), which received inactivated combined vaccine at 0 and 2 weeks of age, and the control group (n = 53), which received no vaccine. From both groups, eight calves each were randomly selected to determine the antibody titers. And, the incidence of respiratory disease and medical costs (treatment plus vaccination costs) were recorded for each group from birth to 16 weeks of age. In the vaccination group, the antibody titers against P. multocida, M. haemolytica, and H. somni were significantly higher than those in the control group after 8, 12, and 4 weeks of age, respectively (p < 0.05). The incidence of respiratory disease was significantly lower in the vaccination group compared to the control group (p < 0.01), and the medical costs per calf in the vaccination group were 46.4% lower than in the control group. These results might contribute to establishing an effective vaccination program against respiratory diseases in calves at each farm.