Begonia medicinalis is an Indonesian endemic plant that has been reported to exert multiple pharmacological effects, including antiviral and anticancer activities. These activities have been suggested to be related to the immunomodulatory properties of dried B. medicinalis ethanolic extract (DBME). However, this notion remains unclear. This study was carried out aiming to investigate the immunomodulatory effect of DBME in Drosophila melanogaster model based on the expression of genes in the Toll, Imd, and JAK-STAT pathways. Phenotypical analysis on the survival and locomotor of D. melanogaster was carried out to reveal whether changes in the gene expressions were observable at the phenotypical level. Four groups of D. melanogaster were prepared and treated with DBME (0%, 0.25%, 0.5%, and 2%). The results demonstrated that DBME could modulate the expression of Drs (Toll pathway), Dpt (Imd pathway), and TotA (JAK-STAT pathway) in D. melanogaster. These molecular changes were accompanied by almost no changes in survival and locomotor activities. In brief, DBME can induce the humoral immune responses of D. melanogaster without significant phenotypical trade-offs.