The two European officials, who attended the Group of Seven summit in Hiroshima, are making their first visits to the East Asian country, to discuss topics including trade deals, the war in Ukraine and North Korea's banned weapons programs.
"The European Union and South Korea are expected to express their joint strong support for upholding the rules-based international order," the European Council said in a statement.
South Korea, the world's ninth largest arms exporter, has sent humanitarian aid to Ukraine and sold tanks and howitzers to Kiev's ally Poland, which is fighting off a Russian invasion.
But it implements a policy that prevents it from supplying weapons to conflict areas.
Yoon held talks with President Volodymyr Zelensky on the sidelines of the Group of Seven summit Sunday, after meeting with his wife Olena Zelenska in Seoul last week.
During his meeting with Zelensky in Hiroshima, Yoon promised non-lethal assistance to Ukraine, including mine-clearing equipment and ambulances, at the Ukrainian president's request, according to the South Korean presidential office.