Large deep-sea fans are useful settings to study gas hydrate systems, the rapid burial of organic-rich sediment driving linked processes of gas generation, fluid expulsion and syn-sedimentary tectonism. The Nile deep-sea fan (100,000 km2) is a collapsing Late Cenozoic depocentre that is both a hydrocarbon province and an area of widespread seafloor fluid seepage. Evidence for gas hydrates has been reported in this area, but remains poorly documented. Available seismic and well data are used together with information on seafloor features to characterise a deep-water (1500–2700 m) gas hydrate system in the central Nile fan. The system is in part expressed as a bottom simulating reflection (BSR) discontinuously observed across a relatively small area (6000 km2), both cross-cutting the stratified fill of fault-bound slope basins, and upslope of the basins within thick unstratified mass transport deposits. West of the BSR area, log data from two wells 45 km apart indicate the presence of gas hydrates in intervals up to 75 m thick near the base of the stability zone. Gas hydrates are also likely to be present near the seafloor within hundreds of pockmark-like mounds that record gas venting through the stability zone, most observed west of the BSR area. The central Nile fan thus contains a gas hydrate system expressed as two areas of comparable size, one with a discontinuous BSR but few seafloor gas vents, another lacking a BSR but with downhole evidence of gas hydrates and abundant gas venting. This heterogenous character is suggested to reflect spatial variations in fluid expulsion from the Nile fan, which can inhibit BSR formation while favouring gas hydrate accumulation over wide areas. This possibility has implications for other large deep-sea fans, many of which have restricted BSRs but may contain more extensive gas hydrate systems.