Different carbon nanomaterials are considered as promising supports for Fischer-Tropsch synthesis (FTS) catalysts of syngas transformation into hydrocarbons. At the same time, consolidation of carbon nanoparticles into a dense bulk material is one of the most important challenges faced by the catalytic industry. In this work consolidated Co and Fe catalysts supported on graphene nanoflakes (GNFs) were for the first time synthesized by spark plasma sintering (SPS). The synthesized catalysts contained reduced carbon-encapsulated metal nanoparticles embedded into the GNF framework, which ensured their activity in FTS without pre-activation. SPS significantly increased both the activity (from 77 to 91 µmolCO×gCo−1 ×s−1) and TOF (from 0.024 to 0.073 s−1) of the Co/GNF catalyst compared to the unsintered sample. In contrast, the activity of the Fe catalysts decreased after SPS, but their C5+ selectivity and olefins to paraffins ratio increased. These enhancements were attributed to the unique core-shell structure of the nanoparticles, highly active surface cobalt atoms, and close contact between carbon support and iron particles. SPS was proved to be a powerful approach to activate carbon-supported FTS catalysts, increase their density and modify their catalytic performance.