The aim of the present study was to assess the ultrastructural alterations of juvenile Schistosoma japonicum induced by mefloquine. Mice infected with 14-day-old S. japonicum were treated orally with mefloquine at a single dose of 400 mg/kg. Between 8 h and 7 days after treatment, groups of two mice were sacrificed, and schistosomula were recovered for transmission electron microscopic observations. Ultrastructural damage was seen in the tegument, subtegumental musculature, parenchymal tissues, and gut epithelial cell. It was already prominent 8 h after drug administration and increased in severity rapidly to reach a peak 3 days post-treatment. Tegumental alterations were characterized by emergence of irregular and elongated cytoplasmic processes, which further fused together accompanied by indistinction of matrix and roughness of external plasma membrane. Meanwhile, in the subtegument, damage to the syncytium, swelling, and lysis of muscle bundles and parenchymal tissues were universal, which further aggravated the lesion on the tegument, followed by collapse or disintegration of damaged tegument to form numerous fragment or debris of cytoplasmic process detached from the worm surface. Severe damage to the gut epithelial cell was also observed 8 h post-mefloquine treatment, which included focal lysis of cytoplasm accompanied by formation of vacuoles and degeneration of mitochondria, emergence of enlarged and contracted nucleus with indistinct or focal disrupted nuclear membrane, and decrease in microvilli. All these alterations further increased in severity and reached the peak 3 days post-treatment. The findings of our study indicate that mefloquine exhibits a fast and potent ability to cause extensive ultrastructural damage to juvenile S. japonicum, which correlates with its high efficacy against juvenile schistosomes.