Electrochemical energy systems, such as batteries and fuel cells, are being developed for applications ranging from portable devices and electric vehicles to large-scale grid storage. These advanced energy conversion and storage technologies will be a critical aspect of a sustainable energy future and promise to provide cleaner, more efficient energy. Computational modeling at various scales from nanoscale ab initio modeling to macroscale system and controls level modeling, has been a central part of the electrochemical energy research. Much of the complex interactions due to the electrochemistry coupled transport phenomena occur at the interfaces and within the porous electrode microstructures. This is often referred to as the mesoscale and plays a critical role in the operation and efficiency of electrochemical devices. In this critical perspective, we discuss the state-of-the-art, challenges and path forward in mesoscale modeling of electrochemical energy systems and their application to various design and operational issues in solid oxide fuel cells, polymer electrolyte membrane fuel cells, lithium ion batteries and metal-air batteries. Particular focus is given to particle-based methods and fine-scale computational fluid dynamics based direct numerical simulation techniques, along with the challenges and advantages of these methods. Notable results from mesoscale modeling are presented along with discussions of the advantages, disadvantages and challenges facing mesoscale model development. This in-depth perspective is envisioned to serve as a primer to the critical role mesoscale modeling is poised to play in advancing the science and engineering of electrochemical energy systems.