Transfecting foreign genes into target cells require certain vectors and specific techniques. With more new genes and gene targets for gene therapy are continually being discovered, which provide useful clues for the study of gene function and gene therapy for human disease. However, there still remain a number of important unresolved problems associated with the use of viral and non viral vectors or techniques, such as secondary toxicity, immune response, or low gene transfer efficiency. Therefore, efficient and safe approaches of gene delivery in vivo still need to be found for medical applications. Electroporation or ultrasound (US), which involving electrical pulses or a US field to increase cell membrane permeability, has shown to be an efficient, safe and simple non viral physical method of DNA delivery in vivo and alternative technique in the field of gene therapy. However, the high field strength or energy often required for electroporation or US can result in tissue damage, thus limit their widely clinical applications. In recent years, site-specific gene delivery by electroporation or US has aroused much attention, because of optimized protocols and novel devices using a lower field strength than conventional methods, which has shown high transfection efficiency with minimal tissue damage. In this paper, we reviewed the advancement in the field of electroporation and US for gene delivery, particularly by site-specific delivery into skeletal muscle for gene therapy and their applications in Alzheimer’s disease (AD)’s treatment.