Given the threats of climate change, understanding the relationship of climate with long-term population dynamics is critical for wildlife conservation. Previous studies have linked decadal climate oscillations to indices of juvenile recruitment in loggerhead sea turtles (Caretta caretta), but without a clear understanding of mechanisms. Here, we explore the underlying processes that may explain these relationships. Using the eddy-resolving Ocean General Circulation Model for the Earth Simulator, we generate hatch-year trajectories for loggerhead turtles emanating from Japan over six decades (1950-2010). We find that the proximity of the high-velocity Kuroshio Current to the primary nesting areas in southern Japan is remarkably stable and that hatchling dispersal to oceanic habitats itself does not vary on decadal timescales. However, we observe a shift in latitudes of trajectories, consistent with the Pacific Decadal Oscillation (PDO). In a negative PDO phase, the Kuroshio Extension Current (KEC) is strong and acts as a physical barrier to the northward transport of neonates. As a result, hatch-year trajectories remain mostly below 35°N in the warm, unproductive region south of the Transition Zone Chlorophyll Front (TZCF). During a positive PDO phase, however, the KEC weakens facilitating the neonates to swim north of the TZCF into cooler and more productive waters. As a result, annual cohorts from negative PDO years may face a lack of resources, whereas cohorts from positive PDO years may find sufficient resources during their pivotal first year. These model outputs indicate that the ocean circulation dynamics, combined with navigational swimming behavior, may be a key factor in the observed decadal variability of sea turtle populations.