President Barack Obama is the first serving American leader to visit the predominantly-Muslim nation since 1966.
The visit signals closer bilateral relations after decades of uneasy ties.
Barack Obama is expected to seek closer trade relations with Malaysia to dilute China’s influence in the region.
The US has already provided Kuala Lumpur with military assistance, most recently in the search for the missing Malaysian airline.
Barack Obama landed at Malaysia’s Air Force base in Subang on Saturday evening local time.
The US president has already visited Japan and South Korea as part of a four-nation tour of Asia.
Ahead of the visit, Malaysia’s government controlled newspapers printed the American flag on their front pages, along with the words “Welcome, Mr. President”.
But some analysts say it has taken Barack Obama too long to visit Malaysia, especially since he lived in the region as a child.
American presidents had stayed away because of years of anti-Western rhetoric under former Malaysian leader Mahathir Mohamad, but current PM Najib Razak wants Washington to recognize Malaysia as a global player.
In his turn, Barack Obama wants Kuala Lumpur to sign a free trade deal with 10 other nations – the so-called Trans-Pacific Partnership.
Ben Rhodes, Barack Obama’s deputy national security adviser, said relations between the US and Malaysia had blossomed in recent years.
Malaysia has become a “pivotal state” in the Obama administration’s push to strengthen ties throughout the fast-growing and strategically important region, the Associated Press quoted Ben Rhodes as saying.
However, some Malay Muslims claim that the US-led trade deal will reduce their economic privileges over other ethnic groups in the country.
Barack Obama arrived in Malaysia from South Korea and will finish his Asian tour in the Philippines on April 29.
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