Pump-to-wheels (PTW) methane emissions from the heavy-duty (HD) transportation sector, which have climate change implications, are poorly documented. In this study, methane emissions from HD natural gas fueled vehicles and the compressed natural gas (CNG) and liquefied natural gas (LNG) fueling stations that serve them were characterized. A novel measurement system was developed to quantify methane leaks and losses. Engine related emissions were characterized from twenty-two natural gas fueled transit buses, refuse trucks, and over-the-road (OTR) tractors. Losses from six LNG and eight CNG stations were characterized during compression, fuel delivery, storage, and from leaks. Cryogenic boil-off pressure rise and pressure control venting from LNG storage tanks were characterized using theoretical and empirical modeling. Field and laboratory observations of LNG storage tanks were used for model development and evaluation. PTW emissions were combined with a specific scenario to view emissions as a percent of throughput. Vehicle tailpipe and crankcase emissions were the highest sources of methane. Data from this research are being applied by the authors to develop models to forecast methane emissions from the future HD transportation sector.