Combat vehicles have unmet needs for auxiliary power units (APUs) that reduce fuel consumption and offer improved operational effectiveness and soldier safety. Adoption of fuel cell APU technology is hindered by requirements for fuel desulfurization and reforming. Both solid-oxide and polymer-electrolyte-membrane fuel cells are poisoned by sulfur compounds in jet fuels. To more efficiently manage desulfurization processes, improved in-line methods of determining the sulfur content of fuel are required. Mainstream Engineering is developing a compact, in-line analyzer for measuring total sulfur in jet fuel for fuel cell applications. This analyzer enables less frequent desulfurizer regeneration events when compared to scheduling regenerations based on the assumed worst-case sulfur limit. The measurement technique uses multivariate analysis of Raman intensity spectra, which offers calibration robustness, contaminant detection, and identification of fuel type.