A comprehensive emission inventory of the transport sector through fuel-based emission factors (EFs) was developed for the first time in Nepal. This study estimates air pollutants emission from diesel vehicles between the years 1989 and 2018 based on national statistical data, average vehicle kilometers travelled, fuel mileage, and measurement-based EFs for each vehicle category during idle and moving conditions. The consumption of diesel by vehicle category was also estimated and total consumption was compared with national sales data. The Monte Carlo was used to estimate uncertainties. Nationally, total diesel consumption was estimated as 892,770 kL (85–115%) in 2017/18, 13.4 times higher than 1989/90. Ratnoze1 and Microaeth were used to conduct the tail pipe emission measurements. The fuel-based EFs of CO2, CO, BC, and PM2.5 were calculated through the carbon mass balance method. Of all diesel vehicles measured (n = 29) during idling, the average EFs were estimated as CO2 2600 (99–101%), CO 33.3 (44–156%), BC 0.6 (25–101%), and PM2.5 5.2 (0–235%) in unit of g L−1. For moving conditions (n = 5), the average EFs were estimated to be CO2 2476 (90–110%), CO 97.3 (0–232%), BC 1.7 (46–110%), and PM2.5 20.7 (0–255%), all in g L−1. Multiplying fuel consumption by EFs, national air pollutant emissions were estimated as 2214 (90–110%) to 2781(85–115%) for CO2, 27.7 (42–158%) to 88.8 (0–232%) for CO, 0.51 (23–177%) to 3.55 (46–110%) for BC and 3.42 (0–236%) to 23.47 (0–255%) for PM2.5 in 2017/18 in unit of Gg. This paper recommends revising national vehicle mass emission standards based on the findings of this study and including and enhancing sustainable low-carbon transport through amendment of transport policy. © 2021 Elsevier B.V.