Capsaicin and capsiate, which is an analogue of capsaicin, are agonists of capsaicin-binding transient potential vanilloid 1 (TRPV1) receptors. However, their physiological effects are different. Capsaicin induces thermogenesis and nociception, while the different kinetics of capsiate result in thermogenesis without nociception in the oral cavity. In the present study, using functional magnetic resonance imaging, we compared the brain activation after intragastric infusion of non-nociceptive levels of capsaicin and capsiate in wild-type and TRPV1-knockout (KO) mice. Capsaicin activated several brain regions, such as the periaqueductal grey (PAG), thalamic nuclei and hypothalamus, including the medial preoptic area (mPOA) and ventromedial hypothalamus (VMH). Most of these areas were not activated in TRPV1-KO mice. Capsiate activated several regions, including the thalamic nuclei, mPOA and VMH but not PAG in wild-type mice. Most of the activated areas were not activated by intragastric capsiate infusion in TRPV1-KO mice. These results demonstrate that TRPV1 is critical for the induction of activation in the hypothalamus by capsaicin and capsiate, and these distinct brain activations could help to explain the individual physiological reactions of capsaicin and capsiate.