Surface expression levels of high-affinity immunoglobulin E (IgE) receptors (FcεRI) on mast cells are regulated by constitutive internalization from the plasma membrane, which is thought to be an important determinant of FcεRI-mediated signaling potential. However, molecular mechanism of FcεRI trafficking has remained poorly understood. Rab proteins are small guanosine 5′-triphosphatases (GTPases) involved in the regulation of membrane traffic. In particular, Rab5 has been shown to regulate transport in the early endocytic pathway, whereas it is not known whether the FcεRI surface expression levels are regulated by Rab5. In this study, we investigated the role of individual Rab5 isoforms in mast cells by small interfering RNA knockdown method. Our results demonstrate that Rab5a knockdown enhanced FcεRI-dependent mast cell activation and upregulated FcεRI surface expression in its steady state. In contrast, Rab5c knockdown caused suppression of the activation. These findings revealed modulatory and individual roles of Rab5 isoforms in mast cell functions.