This study identified the formal kinetics of aerobic oxidation of the paraffin-naphthenic fraction of diesel fuel in the presence of multi-walled carbon nanotubes (MWCNTs) containing three transition metals—Fe, Co, and Mn. The synthesis of metal-containing multi-walled carbon nanotubes (M@MWCNTs) was carried out by pyrolysis of cyclohexane in the presence of ferrocene (CVD synthesis), followed by sequential doping of the resulting iron-containing carbon nanotubes Fe@MWCNTs with Co and Mn clusters. The resulting Fe–Co–Mn@MWCNT samples were identified using electron microscopy (SEM, TEM) and elemental analysis. The resulting carbon nanotubes were found to have a diameter of 30–60 nm and length of 500–800 μm. Iron clusters were observed to be present within the channels, while Co and Mn particles were observed to be present in the outer space of the nanotubes. The formal kinetic regularities of the dearomatized diesel fraction aerobic oxidation promoted by M@MWCNT additives were studied. It has been demonstrated that metal-nanocarbon additives effectively catalyze the oxidation process in the absence of hydroperoxides, resulting in thermal decomposition. The introduction of Co and Mn clusters into the nanotube structure has been observed to enhance catalytic activity. A catalytic oxidation scheme is currently under consideration, with corresponding effective oxidation rates being determined. It is postulated that these findings may prove useful in the estimation of effective nano-catalytic systems for the oxidative conversion of multicomponent hydrocarbon feedstocks.