The temperature dependences of the kinematic viscosity during heating and cooling have been investigated in Co-B melts with a boron content of up to 30.8 at. A liquid–liquid structural transition was found, which is accompanied by an increase in the activation energy and cluster size, as well as a significant decrease in the density of the melt. The liquid–liquid structural transition was associated with the formation of clusters with a short-range order of Co23B6 in the intermediate temperature region. At low and high temperatures, clusters of the order of an atomic size are active participants in the viscous flow. It was shown that with an increase in the cluster size, the activation energy increases and the viscosity of melts decreases. The formation of large Co23B6 clusters during the cooling of melt with low boron content leads to undercooling and the appearance of the transition temperature region with high activation energy, although this region does not exist during the heating stage.