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Enzootic bovine leukosis caused by the bovine leukemia virus (BLV) results in substantial damage to the livestock industry; however, we lack an effective cure or vaccine. <i>BoLA-DRB3</i> polymorphism in BLV-infected cattle is associated with the proviral load (PVL), infectivity in the blood, development of lymphoma, and in utero infection of calves. Additionally, it is related to the PVL, infectivity, and anti-BLV antibody levels in milk. However, the effects of the <i>BoLA-DRB3</i> allele and BLV infection on dairy cattle productivity remain poorly understood. Therefore, we investigated the effect of BLV infection and <i>BoLA-DRB3</i> allele polymorphism on dairy cattle productivity in 147 Holstein dams raised on Japanese dairy farms. Our findings suggested that BLV infection significantly increased milk yield. Furthermore, the <i>BoLA-DRB3</i> allele alone, and the combined effect of BLV infection and the <i>BoLA-DRB3</i> allele had no effect. These results indicate that on-farm breeding and selection of resistant cattle, or the preferential elimination of susceptible cattle, does not affect dairy cattle productivity. Additionally, BLV infection is more likely to affect dairy cattle productivity than <i>BoLA-DRB3</i> polymorphism.