Migration allows animals to track the environmental conditions that maximize growth, survival, and reproduction [1–3]. Improved understanding of the mechanisms underlying migrations allows for improved management of species and ecosystems [1–4]. For centuries, the catadromous European eel (Anguilla anguilla) has provided one of Europe's most important fisheries and has sparked considerable scientific inquiry, most recently owing to the dramatic collapse of juvenile recruitment [5]. Larval eels are transported by ocean currents associated with the Gulf Stream System from Sargasso Sea breeding grounds to coastal and freshwater habitats from North Africa to Scandinavia [6, 7]. After a decade or more, maturing adults migrate back to the Sargasso Sea, spawn, and die [8]. However, the migratory mechanisms that bring juvenile eels to Europe and return adults to the Sargasso Sea remain equivocal [9, 10]. Here, we used a “magnetic displacement” experiment [11, 12] to show that the orientation of juvenile eels varies in response to subtle differences in magnetic field intensity and inclination angle along their marine migration route. Simulations using an ocean circulation model revealed that even weakly swimming in the experimentally observed directions at the locations corresponding to the magnetic displacements would increase entrainment of juvenile eels into the Gulf Stream System. These findings provide new insight into the migration ecology and recruitment dynamics of eels and suggest that an adaptive magnetic map, tuned to large-scale features of ocean circulation, facilitates the vast oceanic migrations of the Anguilla genus [7, 13, 14].