Bats are the only active flying placental mammals and are traditionally classified into mega- and microbats, which are, respectively, herbivorous and insectivorous in feeding habit. Though deforestation, habitat destruction, natural calamities, illegal hunting, and climate changes are the challenging threats for bats, the role of existing gastrointestinal (GI) parasites have not been evaluated yet in Nepal. Thus, the current study aims to determine the prevalence of GI parasites in bats from the Shaktikhor area at the Chitwan district of Southcentral Nepal. From July 2018 to February 2019, a total of 60 fecal samples of bats (30 from frugivorous bats and 30 from the insectivorous bats) were collected. These samples were preserved at 2.5% potassium dichromate solution. The fecal examination was carried out by the direct wet mount, concentrations, acid-fast staining, and sporulation techniques. Overall results showed the prevalence rate of 80% GI parasites. The parasites detected in the insectivorous bats were Ascarid spp., Capillarid sp., Cryptosporidium sp., Eimeria spp., Entamoeba sp., Giardia sp., Hymenolepis spp., Isospora sp., Oxyurid sp., Strongyle, and Strongyloides sp. In contrast, Eimeria sp., Entamoeba sp., and Hymenolepis sp. were detected in the frugivorous bats. Based on a wide diversity of parasite richness and parasitic concurrency measured by the prevalence rates, we suggest that GI parasitism might be a threatening factor in the insectivorous bats in the current study area.