To significantly reduce the cost of proton exchange membrane fuel cells, platinum-group metal (PGM)-free cathode catalysts are highly desirable. Current M-N-C (M: Fe, Co or Mn) catalysts are considered the most promising due to their encouraging performance. The challenge thus has been their stability under acidic conditions, which has hindered their use for any practical applications. In this review, based on the author’s research experience in the field for more than 10 years, current challenges and possible solutions to overcome these problems were discussed. The current Edisonian approach (i.e., trial and error) to developing PGM-free catalysts has been ineffective in achieving revolutionary breakthroughs. Novel synthesis techniques based on a more methodological approach will enable atomic control and allow us to achieve optimal electronic and geometric structures for active sites uniformly dispersed within the 3D architectures. Structural and chemical controlled precursors such as metal-organic frameworks are highly desirable for making catalysts with an increased density of active sites and strengthening local bonding structures among N, C and metals. Advanced electrochemical and physical characterization, such as electron microscopy and X-ray absorption spectroscopy should be combined with first principle density functional theory (DFT) calculations to fully elucidate the active site structures.