Neoclassical realism theory holds that a nation’s foreign policy is the result of international systemic stimuli intervened by domestic variables. It provides a suitable theoretical framework for analysing the changes of Japan’s foreign policy towards Israel. For a long time after World War II, the relations between Japan and Israel remained cold mainly under the system constraints and its contradictions with domestic variables. However, since Abe’s second term in power, Japan has significantly strengthened its diplomatic relations with Israel. The changes both in the Middle East regional system and the global system have stimulated the adjustment of Japan’s policy while the domestic variables have responded to systemic stimuli actively. Japan’s strengthening of relations with Israel is reflected in several aspects, including high-level political visits, innovative industrial cooperation, and people-to-people cultural diplomacy. On the whole, Japan’s development of relations with Israel serves the interests of both countries and has had a certain impact on the international system. However, there are obvious limitations to Japan’s intensifying diplomacy with Israel.