Through data mining of the Cordyceps militaris genome, a lectin-encoding gene, CMLec3, was identified. In this study, the CMLec3 sequence was analyzed using bioinformatics approaches, and the gene was heterologously expressed in Escherichia coli BL21 cells. The biological activity of the product was examined. In addition, CMLec3 gene expression levels were assessed. The results showed that the CMLec3 protein contained a lectin domain structure and was successfully expressed. The CMLec3 protein partly inhibited HeLa cell proliferation. CMLec3 exhibited the highest gene expression in the primordium at a level 5.19 times that of the mycelium and 1.35 times that of the fruiting body. This suggests that the gene may be related to fruiting body development.