Per- and polyfluoroalkyl substances (PFASs) have been detected in the remote Arctic Ocean. However, due to their complex transport mechanisms and the limited understanding of emerging PFASs in the region, further exploration is necessary. This study comprehensively investigated the vertical profile of both traditional and emerging PFASs in the central Arctic Ocean. The highest concentrations of PFASs were observed in surface seawater, suggesting continuous input into the remote Arctic Ocean. Perfluorobutanoic acid (PFBA) and perfluorooctanoate (PFOA) were the predominant compounds in surface waters. The frequent detection of hexafluoropropylene oxide-dimer acid (HFPO-DA) indicated a shift from traditional PFASs to emerging compounds. In the interior Arctic basin, PFAS concentrations generally decreased with depth, with notable presence in deep water masses (1,000 m), a significant deviation from previous findings that restricted PFASs to the halocline (above 150 m). This suggests that PFASs are penetrating into Atlantic water masses through the biological pump, particulate settling, and vertical advection. In contrast, the lowest PFAS levels were found in the subsurface layer (~100 m) of the Chukchi Plateau, likely linked to the inflow of Pacific Water with the absence of perfluoroalkyl sulphonic acids (PFSAs). This study highlights the persistence and cycling of traditional and emerging PFASs in the remote Arctic.