Although metabolomics studies are recently spreading and have allowed the characterization of putative biomarkers in many diseases, they are relatively scanty in anorexia nervosa (AN). In this explorative study we analyzed the fecal metabolomics profiles of women with AN in the underweight phase (n = 24) and after short-term weight restoration (n = 16) and compared them with 20 healthy women. An untargeted metabolomic procedure allowed the characterization of 224 metabolites involved in energy, lipid, and amino acid metabolism. A partial least square discriminant analysis identified 14 metabolites with a variable importance in projection score >1.5 that clearly differentiated underweight from weight-restored patients from healthy women. Compared with healthy women, fecal concentrations of valeric acid and 3-methyl,2-ketobutyric acid were increased in both underweight and weight-restored patients; fecal concentrations of propionic acid, stearic acid, linolenic acid, methyl-galactoside, coprosterol, cycloserine, and lauric acid were increased while fecal levels of xylose, fucose, and rhamnose were decreased in underweight patients and normalized after weight-restoration; fecal concentrations of piperine, phenylalanine, butyric acid, and meso-erythritol-1 were decreased while fecal levels of hydroxystearic acid were increased in weight-restored but normal in underweight AN patients. All these changes point to peculiar fecal metabolomics profiles of acute and short-term weight restored AN patients. The value of these changes to improve our understanding of the pathophysiology of AN and to characterize potential biomarker targets for developing new treatment strategies needs further studies to be clarified.