Stoneflies (order Plecoptera), one of the earliest winged insects, are ecologically vital as freshwater bioindicators. Despite their ecological and evolutionary significance, a robust phylogeny for stoneflies has remained elusive. Here, we analyzed mitogenomes from 97 species representing all 17 families, employing site-heterogeneous models to reconstruct a comprehensive phylogeny of global Plecoptera. Our results provide several key insights: 1) Scopuridae is the earliest diverging lineage within Euholognatha; 2) Taeniopterygidae and Leuctridae form sister groups, representing the second diverging clade within Euholognatha; 3) Capniidae is resolved as the sister group to Nemouridae + Notonemouridae; and 4) the phylogenetic relationships within Systellognatha are resolved. Furthermore, by integrating palaeontological and chronostratigraphic data, we selected well-vetted fossil calibrations to reconstruct a temporal framework for Plecoptera evolution. Our study identifies key periods in Plecoptera's early divergence and the origins of extant stonefly families, establishing a foundation for future research into their biogeography, morphology, and behavioral evolution.