Much progress has been made in gene therapy, but significant challenges remain. One is development of a range of different tools that can be used for different therapeutic purposes. Another is site-specific gene targeting for safe and faithful therapeutic gene expression. Viruses have long been considered the most promising tools for human gene therapy. However, fatal side effects associated with viral vectors have hampered their clinical application. DNA transposons, widely utilized for decades as genetic tools in plants and insects, are now emerging as viable vectors for gene therapy. In this article, we will give a brief review of the adverse effects associated with virus-based gene therapy followed by a glimpse of the adeno-associated virus vector system, which is currently the most promising viral vector for gene therapy. The development of DNA transposon-based gene delivery systems and the advantages and limits of the most commonly used DNA transposon systems, Sleeping Beauty, Tol2, and piggyBac, will be extensively discussed Finally, we will focus on the most promising transposon system for gene therapy, piggyBac. Challenges and considerations for advancing piggyBac for therapeutic application will be critically addressed.