Spatial and temporal ambient temperature variations directly influence cellular biochemistry and thus the physiology of ectotherms. However, many aquatic ectothermic species maintain coordinated sensorimotor function during large acute body temperature changes, which points to a compensatory mechanism within the neural system. Here, we used high-resolution functional magnetic resonance imaging to study brain responses to a drop of 10°C of ambient water temperature in common carp. We observed a strong drainage of blood out of the brain as of 90 s after the onset of the temperature drop, which would be expected to reduce entry of cold blood arriving from the gills, so that the change in brain temperature would be slower. Although oxygen content in the brain thus decreased, we still found specific activation in the preoptic area (involved in temperature detection and stress responses), the pituitary pars distalis (stress response), and inactivation of the anterior part of the midbrain tegmentum and the pituitary pars intermedia. We propose that the blood drainage from the brain slows down the cooling of the brain during an acute temperature drop. This could help to maintain proper brain functioning including sensorimotor activity, initiation of the stress response and the subsequent behavioral responses.