Asenapine (ASE) is a novel atypical antipsychotic used in schizophrenia treatment. Here, the effect of ASE on Fos expression in hypocretin (Hcrt) neurons in medial and lateral portions of the lateral hypothalamus (LH) and the effect of chronic unpredictable variable mild stress (CMS) preconditioning were studied. CMS consisted of restraint, social isolation, crowding, swimming, and cold and lasted 21 days. The rats were sacrificed on day 22, 90 min after a single injection of vehicle (saline 300 μl/rat subcutaneously--s.c.) or ASE (0.3 mg/kg s.c.). Control (CON), ASE, CMS, and CMS+ASE groups were used. Fos protein was visualized by the avidin biotin peroxidase technique, while Hcrt perikarya by fluorescent dye. Fos/Hcrt co-localizations were evaluated under parallel light and fluorescent illuminations. In the single Fos expression assessment, the Fos number was significantly higher in the medial in comparison with the lateral LH portion in each group. No differences in Fos amount were observed between the individual groups within the medial and lateral LH portions. In the Fos/Hcrt co-localization assessments, ASE significantly reduced the number of Fos/Hcrt neurons in the medial, but not lateral, LH portion in ASE and CMS+ASE groups. CMS only slightly contributed to the inhibitory effect of ASE in the CMS+ASE groups. The present data show as the first that ASE may reduce the activity of Hcrt cells in the medial LH portion, which might correspond with the relatively low weight gain liability of ASE. CMS preconditioning did not significantly interfere with this impact of ASE.