Although reining in North Korea's nuclear programme will top Kerry's agenda during his brief visit, the currently toxic state of Seoul's ties with Tokyo are also a matter of concern to Washington.
South Korea and Japan are the main US military allies in Asia, and both are members of stalled six-party talks on North Korea's nuclear ambitions.
"The secretary's strong view is that tensions between these great democracies, between these important economies, between these close partners of the United States in Asia serve nobody's interests," a senior State Department official told reporters travelling on Kerry's plane.
Although Kerry is not in a position to "broker a deal or mediate" between the two countries, "he will certainly encourage his counterparts to ... effectively manage tensions and to ensure continued and enhanced cooperation," the official said.
Kerry's first talks in Seoul will be with President Park Geun-Hye who has ruled out any summit with Japanese Prime Minister Shinzo Abe until he takes steps to address South Korea's historical grievances.
Japan's 1910-45 colonial rule over the Korean peninsula remains a hugely emotive issue in South Korea, which feels successive Japanese governments have failed to apologise properly or atone for abuses committed during the period.
Following Abe's visit to a controversial war shrine in December, his already low favorability rating in South Korea plunged to the same level as North Korean leader Kim Jong-Un, a recent survey showed.
Japanese politicians express exasperation at Seoul's repeated requests for contrition, pointing to numerous apologies and a 1965 agreement that normalised relations and included a large payment.
The two countries are also involved in a territorial spat over a tiny set of islets, currently controlled by South Korea.
President Barack Obama is to visit both Japan and South Korea during a tour of the region in April.