A major neuroendocrinological effect of calorie restriction (CR) is induction of neuropeptide Y (NPY) in the arcuate nucleus (ARC). Aside from its appetite-stimulating effects, NPY is thought to be involved in the modulation of behavioral processes including anxiety and learning and memory. In the present study physical fitness, anxiety, and learning/memory-related tasks were assessed in mice lacking NPY or a functional ARC after dietary manipulation by CR. Physical fitness was improved by CR when measured by inclined screen and rotarod, and this diet effect was not affected by NPY or ARC status. As has been observed previously, the NPY knockout mice displayed heightened anxiety in an open field. This phenotype was not fully recapitulated in the ARC-lesioned model. CR affected neither total locomotor activity in the open field nor thigmotaxic behavior in these models. Neither NPY nor CR had a significant effect on Morris water maze performance; however, ARC-damaged mice were unable to learn the task, and this deficit was not corrected by CR. We conclude that despite established effects of CR on ARC signaling, our results suggest a mechanistic separation between the two where behavior is concerned.