Abstract We investigate full vector paleomagnetic changes recorded in high‐resolution sediments of Petermann Fjord, North Greenland, deposited over the last 6 kyr, in the context of the recent rapid changes in the geomagnetic field. A Paleomagnetic Secular Variation (PSV) stack (inclination, declination, and relative paleointensity) was reconstructed using four marine sediment cores with an independent age model constrained by seven radiocarbon ages. Magnetic investigations demonstrate that the paleomagnetic signal is carried by low coercivity ferrimagnetic minerals and is well reproduced in all cores, attesting to the quality and reliability of the paleomagnetic recording of these sediments. This signal is broadly consistent in directional changes with distant records in North America and the northern North Atlantic at centennial and millennial timescales, and has millennial scale intensity variations that are consistent with model predictions. The offset between a magnetization age determined through comparison with a northern North Atlantic PSV reference curve, GREENICE, and the radiocarbon age model indicates either a reasonable lock‐in depth of magnetization (∼11 cm from the coretop) or centennial‐scale reservoir age variation through time in the fjord. Reconstructed virtual geomagnetic pole (VGP) migration for the last 6 kyr shows that the recent migration of the magnetic North Pole is consistent with secular paleomagnetic variations on geologic timescales. Our results suggest that magnetic field intensity variations (temporal and spatial) are linked to magnetic flux lobe dynamics and influence the VGP migration.