The Great East Japan Earthquake on 11 March 2011, followed by the tsunami and fire, resulted in serious environmental problems in and around Japan. A huge amount of material was discharged into the ocean after the tremendous flood damage of the tsunami. A monitoring survey of the perfluoroalkyl substances (PFAs) found evidence showing an abrupt increase in the PFA concentration in the ocean east of Japan in 2011 after the earthquake. To confirm the anomalous input of two typical PFAs, perfluorooctanoate (PFOA) and perfluorooctanesulfonate (PFOS), from the Japanese coast into the ocean, associated with the earthquake, we conducted a series of chemical tracer simulations using an eddy-resolving ocean reanalysis product: JCOPE2. The simulation model involves processes representing the emission of PFAs from the land triggered by the tsunami flood, advection of the polluted waters, and decay of the concentration by the background oceanic turbulence. Comparison of the PFOA simulation results with the observation confirms a spike-like input of PFOA into the Western North Pacific after the earthquake. Advection and diffusion by the Kuroshio Extension and the mesoscale eddies play a key role in the dilution of the concentration. Optimization of unknown simulation parameters leads to an estimation of the total amount of the anomalous PFOA emission. In contrast, the PFOS simulations are not able to explain the observed distribution, suggesting possible differences in the oceanic transport processes between PFOS and PFOA.