The hydrogen economy holds significant importance for both the Japanese and Korean governments due to its eco-friendliness, economic feasibility, and role in enhancing energy security. With the escalating climate crisis, mounting pressures to reduce greenhouse gas emissions, and challenges such as supply issues and unstable energy security amid diplomatic tensions between the USA and China, there is a growing impetus for bilateral and multilateral regional cooperation in transitioning to a hydrogen-based economy. In response to these dynamics, Korea and Japan should actively explore collaborative strategies within the hydrogen economy. This study aims to assess the strengths, weaknesses, opportunities, and risks of bilateral cooperation between Korea and Japan in this field, drawing on empirical interviews with policy experts from both countries. Specifically, the study investigates differences and similarities in their perceptions. This study proposes strategies for enhancing bilateral cooperation in the hydrogen economy based on the findings. The insights derived from this study are expected to be valuable for guiding future partnerships in both bilateral and multilateral contexts within the hydrogen economy.