The Jan Mayen Channel is located North of the Jan Mayen Island in the Nordic Seas, and is an important gateway for the exchanges of volume, heat and freshwater between the Greenland and the Norwegian basins via the Jan Mayen Current. Based on observations from moored instruments deployed on the shelf and the continental slope of the Jan Mayen Island from August 2017 to August 2018, we document the mean state and the variability of the currents, temperature and salinity and their associated vertical structure. We found that the main feature of circulation is an intense and permanent south‐eastward jet‐like current centered at 150 m depth, located on the 400 m depth slope, with a maximum mean magnitude of 7 cm·s−1. While the velocities recorded on the shelf are largely constant in speed and direction, without any strong seasonal cycle, the moorings located offshore are capturing larger anomalies on short time scales that are likely the signature of eddies passing across the mooring array. Overall, the variability of the transport across the section is correlated with the large‐scale wind pattern over the Nordic Seas, highlighting that the Jan Mayen Current is part of a complex system of currents that operates at larger scale in the region.