Unlike its mainland relatives, the Japanese pagoda was no longer the centerpiece of the temple, but was often a secondary building. In Japan, the main temple hall held the statue of the Buddha, not the pagoda. As the Japanese altered the purpose of the pagoda, they also continued to alter the architectural methods, as the Chinese had done.

While the stupas of of India were made mainly of stone, the Chinese first made pagodas out of wood. However, a vast majority of Chinese pagodas were made in stone. In Japan, however, the vast majority were made out of wood, with stone pagodas being mainly small models used in gardens. Also, the overhangs on the roofs of the Chinese pagodas were relatively small. However, when one observes the Japanese Pagodas, you can see that the size of the roofs greatly increased. The pagoda to the right is evidence of this expansion. 

Until the introduction of Buddhism in 538 CE, Japan was a nation imbedded in the Shinto religion. However, once Buddhism was introduced to Japan, it quickly took hold with the ruling class. In 594 CE, Prince Shotoku made an imperial decree promoting Buddhism. Thirteen years later, Prince Shotoku started the building of Horyuji Temple. The temple was the first of its kind in Japan, incorporating the pagoda. Interestingly enough, Horyuji Temple was not actually built by Japanese artisans. Korean architects from the kingdom of Paekche were commisioned to build it. After the completion of this first temple, many new temples followed. In 794 CE, One Million Minature Stupas was built. In 1252 CE, the statue of the Amida Buddha was built. In 1339 CE, the Saiho-ji Temple was built, shortly followed by the Golden Pavillon in 1397 CE.