The combination of advanced combustion with advanced selective catalytic reduction (SCR) catalyst formulations was studied in the work presented here to determine the impact of the unique hydrocarbon (HC) emissions from premixed charge compression ignition (PCCI) combustion on SCR performance. Catalyst core samples cut from full size commercial Fe- and Cu-zeolite SCR catalysts were exposed to a slipstream of raw engine exhaust from a 1.9-liter 4-cylinder diesel engine operating in conventional and PCCI combustion modes. The zeolites which form the basis of these catalysts are different with the Cu-based catalyst made on a chabazite zeolite which has smaller pore structures relative to the Fe-based catalyst. Subsequent to exposure, bench flow reactor characterization of performance and hydrocarbon release and oxidation enabled evaluation of overall impacts from the engine exhaust. The Fe-zeolite NOX conversion efficiency was significantly degraded, especially at low temperatures (≺250°C), after the catalyst was exposed to the raw engine exhaust. The degradation of the Fe-zeolite performance was similar for both combustion modes. The Cu-zeolite showed better tolerance to HC fouling at low temperatures compared to the Fe-zeolite but PCCI exhaust had a more significant impact than the exhaust from conventional combustion on the NOX conversion efficiency. Furthermore, chemical analysis of the hydrocarbons trapped on the SCR cores was conducted to better determine chemistry-specific effects.