Duck Tembusu virus (DTMUV), an emerging avian pathogenic flavivirus, causes severe neurological disorders and acute egg drop syndrome in ducks. Currently, several clusters of DTMUV, including clusters 1, 2, and 3, have been identified and caused outbreaks in Asia. However, most of the DTMUV pathogenesis evaluation has mainly focused on cluster 2, while limited information is available on the pathogenesis of other DTMUV clusters, particularly cluster 1. In this study, the pathogenesis of a cluster 1 DTMUV was investigated in Cherry Valley ducks and compared to our previously reported cluster 2.1 DTMUV. Our results demonstrated that cluster 1 DTMUV was generally less pathogenic than cluster 2.1 DTMUV in ducks as evidenced by slower body weight loss, lower morbidity and mortality rates, and milder pathological changes. Concordantly, delayed viremia, reduced viral loads in blood and tissues, and shorter shedding period with lower viral loads were also observed in cluster 1 DTMUV inoculated ducks compared with those reported in cluster 2.1 DTMUV. In addition, we also found that cluster 1 DTMUV exhibited significant antigenic difference compared to cluster 2.1 DTMUV. Altogether, our findings suggest distinct pathogenicity and antigenicity between cluster 1 and 2.1 DTMUVs in ducks, highlighting the potential association between DTMUV genotype and pathogenicity/disease severity. This study enhances our understanding of DTMUV pathogenesis in ducks and provides useful information for the design and development of effective DTMUV vaccines.