The two leaders will attend the event while they are in the United States for a summit of the Asia-Pacific Economic Cooperation (APEC) member states in San Francisco next week, Yoon's office said in a statement.
They are expected to discuss technology cooperation between the two countries as well as three-way cooperation with the United States, it said.
Japan's Kyodo news agency reported this week that Kishida was expected to stress the importance of cooperating on the sourcing of semiconductors and strategic minerals, and on developing artificial intelligence technology.
Yoon has made it a priority to mend ties with Japan since taking office in May 2022, and to restore trilateral security cooperation with the United States as North Korea ramps up its weapons programs and openly threatens the South.
This year, Yoon visited Japan and pledged at a summit with Kishida to turn the page on years of animosity, as Tokyo lifted four years of export curbs on key high-tech materials.
In a controversial move at home, Yoon had pushed ahead with a plan to compensate Korean victims of forced labour under Japan's 1941-45 occupation, seeking to end a dispute that stood in the way of closer ties between the neighbours.
Yoon and Kishida held a summit with U.S. President Joe Biden in August, pledging to deepen military and economic cooperation and restore an alliance aimed at countering North Korea's threats as well as China's growing influence.
The three countries have since conducted joint military drills and agreed on an early warning data sharing on North Korea's missile launches.
(Reporting by Jack KimEditing by Ed Davies and Gerry Doyle)