This study analyzes the intra-industry trade (IIT) patterns between Indonesia and Japan in manufactured and agricultural products and explores its determinants. As one of the biggest importers of Indonesian products, it is expected that Japan has a big influence on the IIT between Japan and Indonesia. The Asian financial crisis, as one determinant, disrupted the extent of intra-industry trade between Indonesia and Japan. To reduce trade barriers, economic agreements such as those found in the Asia Pacific Economic Cooperation had a positive effect on bilateral intra-industry trade between the two countries. In simulations, the bilateral trade policies imposed yielded significant benefits to encourage bilateral intra-industry trade between Indonesia and Japan.