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The flame ionization detector is a standard instrument for measuring total hydrocarbon concentration in engine exhaust. Engine combustion modes such as diesel low-temperature combustion are known to produce higher levels of total hydrocarbon than conventional combustion modes, and a need exists to estimate species that may nucleate into nanoparticles upon dilution in the atmosphere. Exhaust hydrocarbon fractionation is useful for gaining better understanding about engine combustion and for developing aftertreatment catalysts for reducing emissions. Methods capable of measuring individual hydrocarbon species such as gas chromatography and Fourier transform infrared spectrometry do not measure the full range of species present in engine exhaust and are expensive. In this work, a custom-designed variable temperature sample conditioner was developed for use with two fast-response flame ionization detectors to fractionate the hydrocarbons present in engine exhaust as a function of component volatility. A condensation model for fuel alkanes was also developed to be used in concert with the experimental data to determine the fraction of fuel-like hydrocarbons within the total hydrocarbon measurement. Our results indicate that the variable temperature flame ionization detector method yields similar unburned hydrocarbon fraction to reported literature values using more extensive speciation studies at similar engine conditions. We find that while low-temperature combustion engine operation emits higher concentrations of total hydrocarbon than conventional combustion modes, the fraction of less volatile hydrocarbon species is higher for lower engine load, regardless of the combustion mode.