With higher volatility and longer ignition delay characteristics than typical diesel fuel, low cetane naphtha fuel has been shown to promote partially premixed combustion and produce lower soot for improved fuel economy. In this study, emission performance of low cetane, low octane naphtha (CN 35, RON 60) as a drop-in fuel was examined on a MY13 Cummins ISX15 6-cylinder heavy-duty on-highway truck engine and aftertreatment system. Using the production hardware and development calibrations, both the engine-out and tailpipe emissions of naphtha and ultra-low sulfur diesel (ULSD) fuels were examined during the EPA’s heavy-duty emission testing cycles. Without any modification to the calibrations, the tailpipe emissions were comparable when using naphtha or ULSD on the heavy duty Federal Test Procedure (FTP) and ramped modal cycle (RMC) test cycles. Overall lower CO2 emissions and fuel consumption were also measured for naphtha due in part to its higher heating value and higher hydrogen to carbon ratio. Engine-out and tailpipe NOx emissions were lower for naphtha fuel at the same catalyst conversion levels and measured particulate matter (PM) emissions were also lower when using naphtha due to its higher volatility and lower aromatic content compared to ULSD. To help assess the potential impact on diesel particulate filter design and operation, engine-out PM samples were collected and characterized at the B50 operating point. A significant reduction in elemental carbon (EC) within the particulate emissions was found when using naphtha compared to ULSD.