Background Schistosomiasis is one of the most significant and prevalent waterborne parasitic diseases. Even though many studies have been reported about schistosomiasis, the dynamics of schistosome in intermediate host snails is little known. In the present study, the dynamics of Schistosoma larvae in infected snails was histologically investigated. Methods To examine the localization of Schistosoma mansoni (S. mansoni) parasites in the snails, Biomphalaria glabrata snails infected with miracidia were harvested and examined by stereoscopic observation. Then, frozen sections were prepared and stained with H&E. Furthermore, immunohistochemical detection of parasites was performed using anti-S. mansoni antibody, and their localization in the snails was analyzed. Results Snails infected with S. mansoni miracidia were harvested at 10 and 56 days post-infection (DPI) and analyzed. In the stereoscopic observations, white spots were observed at 56 DPI, while no spots were observed at 10 DPI. However, histological investigations visualized the larvae specifically in the head-foot area of the snail at 10 DPI. Further, it was observed that the larvae relocated to the hepatopancreas and ovotestis areas at 56 DPI. Conclusions The present study revealed the dynamics of Schistosoma larvae in intermediate snails, shown as the differential localization of S. mansoni larvae at early and late infection stages.