Molecular junctions, where single molecules are bound to metal or semiconductor electrodes, represent a unique architecture to investigate molecules in a distinct nonequilibrium situation and, in a broader context, to study basic mechanisms of charge and energy transport in a many-body quantum system at the nanoscale. Experimental studies of molecular junctions have revealed a wealth of interesting transport phenomena, the understanding of which necessitates theoretical modeling. The accurate theoretical description of quantum transport in molecular junctions is challenging because it requires methods that are capable to describe the electronic structure and dynamics of molecules in a condensed phase environment out of equilibrium, in some cases with strong electron-electron and/or electronic-vibrational interaction. This perspective discusses recent progress in the theory and simulation of quantum transport in molecular junctions. Furthermore, challenges are identified, which appear crucial to achieve a comprehensive and quantitative understanding of transport in these systems.