In this study 129I and 236U concentrations in seawater samples collected onboard R/V Polarstern during the PS100 expedition in the Fram Strait in 2016 are presented. The overall aim of the study was to investigate the distribution of these long‐lived radionuclides along the transect located at 79°N. The combination of both radionuclides was used for the first time in the Fram Strait to trace ocean circulation pathways of Atlantic waters. Results show that both 129I and 236U concentrations as well as 236U/238U ratios are about two times higher (> 600 × 107 at kg(−1), > 20 × 106 at kg(−1), and 2.8 × 10−9, respectively) in the cold and fresh outflowing surface waters from the Arctic Ocean (Polar Surface Water, PSW) compared to inflowing Atlantic origin waters (300 × 107 at kg(−1) 129I, 12 × 106 at kg(−1) 236U, and 1.4 × 10−9 236U/238U). A comparison with the different 129I and 236U input functions for the Atlantic branches entering the Arctic Ocean reveals that the middepth Atlantic origin waters outflowing the Arctic Ocean show more influence of the Barents Sea Branch Water than the Fram Strait Branch Water. The high radionuclide concentrations observed in the PSW indicate substantial influence of the Norwegian Coastal Current. This current carries a significantly larger proportion of 129I and 236U releases from European reprocessing plants than the aforementioned Atlantic branches. We estimate surface water transit times from the northern Norwegian Coast through the Arctic to the PSW of 12–19 years, less than for the middepth Barents Sea Branch Water (16–23 years).