The study will take place at the Korean nuclear fusion research facility, South Korea announced.
The Ministry of Education, Science and Technology said the two countries will hold additional talks about the specifics of their cooperation in the nuclear fusion energy sector, Yonhap news agency reported.
South Korea completed the Korea Superconducting Tokamak Advanced Research, a Korean nuclear fusion energy device, in 2007.
"The equipment will be sent over free of charge with Japanese researchers allowed to work side by side with local counterparts," a South Korean official said.
South Korea and Japan, along with the European Union, the United States, Japan, Russia, China and India, are the nations that have aimed to build an operable fusion power test bed by 2016.