The meeting comes days after the US lifted a host of financial and trade embargoes in recognition of dramatic political changes that saw landmark elections sweep Suu Kyi and her party into office after decades of junta rule.
Suu Kyi, the foreign minister, also holds the newly-created position of state counsellor to enable her to steer the government despite a junta-scripted constitution that bars her from the presidency - a role now held by her longtime ally Htin Kyaw.
"He will meet the state counsellor, not the president," he told AFP, explaining that Htin Kyaw is yet to return from a summit in Russia.
According to the US State Department, Kerry's brief trip to Myanmar is to show "support for the new democratically-elected, civilian-led government" as well as to "further democratic and economic reforms".
US President Barack Obama has made two visits to the Southeast Asian nation in recent years, seeking to widen engagement with the country as it embarked on a stunning transition towards democracy after half a century under a repressive military government.
American investment in Myanmar remains relatively small compared to other nations, although some US companies including Coca-Cola and Pepsi, fast food restaurant KFC and carmakers Chevrolet and Ford have already established a sales presence.
Washington rolled back many of its sanctions to reward reforms since the end of outright military rule in 2011, but retains scores of names on its blacklists as it seeks to push further changes and promote human rights.
It opened up all Myanmar banks to American business, while also extending indefinitely permission made in December enabling firms to import through Myanmar's ports and airports - many of which are operated by cronies still on the blacklist.
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