As a new sustainable energy source, ubiquitous mechanical energy has received great attention and was successfully harvested by different types of nanogenerators. Among them, biocompatible nanogenerators are of particular interests due to their potential for biomedical applications. In this review, we provide an overview of the recent achievements in the fabrication and application of biocompatible nanogenerators. The development process and working mechanism of nanogenerators are introduced. Different biocompatible materials for energy harvesting, such as amino acids, peptide, silk protein, and cellulose, are discussed and compared. We then discuss different applications of biocompatible nanogenerators. We conclude with the challenges and potential research directions in this emerging field.