Novel antigenic variant strains of the infectious bursal disease virus (IBDV) classified into genogroup A2d have been found in the western part of Japan since 2017. Novel antigenic variant IBDVs now occur in higher frequencies in poultry houses and have been detected in the eastern part of Japan, indicating the spread of IBDVs despite the usual IBDV vaccination. We isolated a novel antigenic variant IBDV, designated as the B2977CE2C3 strain. The B2977CE2C3 strain had two genogroup A2d specific amino acids—lysine and isoleucine, at 221 and 252 aa—along with the other genogroup A2 common amino acids in the projection domains of the VP2 protein corresponding to the virus-neutralizing epitopes and viral pathogenicity. Experimental infection of the B2977CE2C3 strain did not produce any apparent clinical signs in the specific-pathogen-free chickens during the observation period (21 days), but atrophy of the bursa of Fabricius (BF) was apparent. The mean BF to the body weight ratio was 0.35 in negative control chickens at 21 days post-infection (pi) but 0.06 in the B2977CE2C3 infected group. An extremely high copy number of the IBDV genome (>108 copies/µL) was observed in the BF at 3 days pi, while a high copy number of the IBDV genome (>106 copies/µL) was observed in the thymus, spleen cecal tonsil, and bone marrow even though macroscopic lesions were not apparent in these organs.