Agricultural headwater ditches are an important source of indirect agricultural nitrous oxide (N2O) emissions, but their contribution is difficult to quantify. In the present study, the static chamber-gas chromatography technique was used for measurement of N2O emissions from vegetated (V, the whole ditch ecosystem) and non-vegetated (NV, the sediment-water interface only) zones in an agricultural headwater ditch in the Central Sichuan Basin in Southwestern China during 2014-2015. Annual N2O emissions from the agricultural headwater ditch were similar to direct N2O emissions from an adjacent N-fertilized purple soil cropland, suggesting nitrogen (N)-enriched ditches are important anthropogenic N2O sources. Mean cumulative N2O emissions during summer and autumn were higher than those in spring and winter. Overlying water nitrate (NO3 (-)-N) concentration and sediment-water interface temperature were primary factors affecting seasonal N2O emissions. Heavy precipitation transported NO3 (-)-N from cropland and increase NO3 (-)-N in the agricultural headwater ditch water, and subsequently stimulate N2O emissions. A literature review of EF5r (the indirect N2O emission factor for rivers) revealed a mean value of 0.23%, similar to our values (0.27%), and also the default value (0.25%) proposed by the Intergovernmental Panel on Climate Change. The number of studies on indirect N2O emissions remains limited, and more in situ measurements are needed to have more accurate values of EF5r.