Fischer-Tropsch (FT) fuels derived from biomass syngas are renewable fuels that can replace conventional petroleum fuels in jet engine and diesel engine applications. FT fuels typically contain a high concentration of lightly methylated iso-alkanes, whereas petroleum derived jet and diesel fuels contain large fractions of n-alkanes, cycloalkanes, and aromatics plus some lightly methylated iso-alkanes. In order to better understand the combustion characteristics of FT and petroleum fuels, this study presents new experimental data for 3-methylheptane and 2,5-dimethylhexane in counterflow diffusion flames. This new dataset includes flame ignition, extinction, and speciation profiles. The high temperature oxidation of these fuels has been modeled using an extended transport database and a novel detailed chemical kinetic model. Additionally, a recently developed mechanism reduction algorithm, i.e., directed relation graph with expert knowledge (DRG-X), is used to generate a skeletal model with adequate chemical fidelity to well predict detailed speciation profiles. The proposed detailed and reduced models show good qualitative and quantitative agreement with the experimental data. The predicted concentrations of species are compared with newly measured and previously obtained data on n-octane and 2-methylheptane to elucidate the effects of methyl branch location and number.