The Fischer–Tropsch heavy fraction is a potential feedstock for transport-fuels production through co-processing with fossil fuel fraction. However, there is still the need of developing new and green catalytic materials able to process this feedstock into valuable outputs. The present work studies the co-hydrocracking of the Fisher–Tropsch heavy fraction (FT-res.) with vacuum gas oil (VGO) at different ratios (FT-res. 9:1 VGO, FT-res. 7:3 VGO, and FT-res. 5:5 VGO) using phonolite-based catalysts (5Ni10W/Ph, 5Ni10Mo/Ph, and 5Co10Mo/Ph), paying attention to the overall conversion, yield, and selectivity of the products and properties. The co-processing experiments were carried out in an autoclave reactor at 450 °C, under 50 bars for 1 and 2 h. The phonolite-based catalysts were active in the hydrocracking of FT-res.:VGO mixtures, presenting different yields to gasoline, diesel, and jet fuel fractions, depending on the time of reaction and type of catalyst. Our results enable us to define the most suitable metal transition composition for the phonolite-based support as a hydrocracking catalyst.