Hypothermia treatment (HT) is the only formally endorsed treatment recommended for hypoxic-ischemic encephalopathy (HIE). However, its success in protecting against brain injury is limited with a number to treat of 7–8. The identification of the target mechanisms of HIE in combination with HT will help to explain ineffective therapy outcomes but also requires stable experimental models in order to establish further neuroprotective therapies. Despite clinical and experimental indications for an endogenous thermoregulatory response to HIE, the potential effects on HIE-induced brain injury have largely been neglected in pre-clinical studies. In the present study we analyzed gray and white matter injury and neurobehavioral outcome in neonatal mice considering the endogenous thermoregulatory response during HIE combined with HT. HIE was induced in postnatal day (PND) 9 C57BL/6 mice through occlusion of the right common carotid artery followed by one hour of hypoxia. Hypoxia was performed at 8% or 10% oxygen (O2) at two different temperatures based on the nesting body core temperature. Using the model which mimics the clinical situation most closely, i.e. through maintenance of the nesting temperature during hypoxia we compared two mild HT protocols (rectal temperature difference 3 °C for 4 h), initiated either immediately after HIE or with delay of 2 h. Injury was determined by histology, immunohistochemistry and western blot analyses at PND 16 and PND 51. Functional outcome was evaluated by Rota Rod, Elevated Plus Maze, Open Field and Novel Object Recognition testing at PND 30–PND 36 and PND 44–PND 50. We show that HIE modeling in neonatal mice is associated with a significant endogenous drop in body core temperature by 2 °C resulting in profound neuroprotection, expressed by reduced neuropathological injury scores, reduced loss of neurons, axonal structures, myelin and decreased astrogliosis. Immediately applied post-hypoxic HT revealed slight advantages over a delayed onset of therapy on short- and long-term histological outcome demonstrated by reduced neuropathological injury scores and preservation of hippocampal structures. However, depending on the brain region analyzed neuroprotective effects were similar or even reduced compared to protection by endogenous cooling during HIE modeling. Moreover, long-term neurobehavioral outcome was only partially improved for motoric function (i.e. Rota Rod performance and rearing activity) while cognitive deficits (i.e. novel object recognition) remained unchanged. These findings emphasize the need to maintain the nesting temperature during the initiation of the pathological insult and highlight the urgency to develop and assess new adjuvant therapies for HT in well-defined experimental models.