This study explores the intrinsic correlation between trade facilitation and the inbound tourism efficiency in Japan based on the data from 2011 to 2019. According to the data from JNTO, Japan's inbound tourism showed a strong dependence on the Asian market, the growth rate of inbound tourists in Europe, America and Oceania increased in recent years. The COVID-19 seriously hindered the Japan's inbound tourism development. The fixed-effect regression indicates that trade facilitation promoted inbound tourism efficiency in markets of different types. The positive effect of trade facilitation on sightseeing market was most significant in Asia. While in Europe, America and Oceania, the inbound business market benefited most from trade facilitation. Trade facilitation amplified the positive effect of Japan's air transportation capacity, international tourism income and visa-free policy on the inbound tourism efficiency, and effectively buffered the negative impact of natural disasters. With regard to the estimated results of sub-indicators of trade facilitation, the improvement of infrastructure, government efficiency, customs environment and technological level all contributed to the increase in Japan's inbound tourism efficiency.