Developing highly active and durable electrocatalysts for cost-effective proton-exchange membrane fuel cells is challenging1–3. Fe/N–C catalysts are among the most promising alternatives to the platinum group metal catalysts, but their activity and durability still cannot meet the performance criteria due to the strong adsorption of oxygenated reaction intermediates and the demetallization of Fe species caused by the Fenton reaction4–8. Here we design and develop a new type of Fe/N–C catalyst that is composed of numerous nanoprotrusions dispersed on two-dimensional carbon layers with single Fe-atom sites primarily embedded within the inner curved surface of the nanoprotrusions. The graphitized outer carbon layer of the nanoprotrusions can not only effectively weaken the binding strength of the oxygenated reaction intermediates, but also reduce the hydroxyl radical production rate. As a result, the Fe/N–C catalyst delivers one of the best-performing platinum group metal-free proton-exchange membrane fuel cell performances, achieving a record high power density of 0.75 W cm−2 under 1.0 bar H2–air with 86% activity retention after more than 300 hours of continuous operation.