Uncertainty in the future atmospheric burden of methane, a potent greenhouse gas, represents an important challenge to the development of realistic climate projections. The Arctic is home to large reservoirs of methane, in the form of permafrost soils and methane hydrates, which are vulnerable to destabilization in a warming climate. Furthermore, methane is produced in the surface ocean and the surface waters of the Arctic Ocean are supersaturated with respect to methane. However, the fate of this oceanic methane is uncertain. Here, we use airborne observations of methane to assess methane efflux from the remote Arctic Ocean, up to latitudes of 82° north. We report layers of increased methane concentrations near the surface ocean, with little or no enhancement in carbon monoxide levels, indicative of a non-combustion source. We further show that high methane concentrations are restricted to areas over open leads and regions with fractional sea-ice cover. Based on the observed gradients in methane concentration, we estimate that sea–air fluxes amount to around 2 mg d−1 m−2, comparable to emissions seen on the Siberian shelf. We suggest that the surface waters of the Arctic Ocean represent a potentially important source of methane, which could prove sensitive to changes in sea-ice cover.