Hydrogen peroxide (H2O2) is an efficient and environmentally friendly oxidant as well as a promising energy-carrier alternative to hydrogen. Its solar light-driven photocatalytic synthesis from H2O and O2 is a high-prospect sustainable alternative to the industrial anthraquinone process. Hybrid Ru-modified graphitic carbon nitride (g-C3N4) catalysts were prepared by thermal polymerisation of melamine/Ru(III) acetylacetonate mixtures, and subsequent thermal exfoliation. Simultaneous Ru incorporation and thermal exfoliation impacted the morphology and the structure of the g-C3N4 sheets, and low-atomicity Ru species with small nanoclusters and single atoms were observed only in the Ru-modified exfoliated g-C3N4 photocatalysts. We demonstrated the potential of a joint thermal exfoliation and modification with Ru to enhance the H2O2 synthesis efficiency of the g-C3N4 photocatalyst under simulated sunlight. A volcano-type behavior was observed with increasing the Ru content, and the best performance was obtained for exfoliated g-C3N4 with an ultra-low Ru content of 0.019 wt.%, that outperformed both its bulk counterpart and the pristine exfoliated reference in terms of initial H2O2 synthesis rate and H2O2 formation rate constant. The enhanced performance was attributed to the presence of highly dispersed low atomicity Ru as well as to more accessible active sites and carrier migration channels. Quenching experiments revealed a mixed reactional pathway involving both two-step one-electron and one-step two-electron O2 reduction in the photocatalytic H2O2 production.