The casually dressed former president arrived in the resort island of Bali with his wife Michelle and their two daughters, a local military commander said.
"They arrived late last night and went straight to the hotel in Ubud," a local military commander, I Gede Widiyana, told AFP.
Obama woke up early and did some exercise in the lush green riverside resort, Widiyana said, but it was not known how the family would spend their time in the quiet and artsy Ubud area.
Obama spent four years until 1970 as a boy in the then sleepy capital of Indonesia after his divorced mother married an Indonesian.
Many Indonesians felt a strong bond with Obama because of his exposure to Indonesia and its culture, even making him a two-metre (six-foot) bronze statue that was placed in his former school.
The statue of "Little Barry" -- as Obama was known to his Indonesian school friends -- depicts the boy Obama dressed in shorts and a T-shirt with a butterfly perched on his hand.
While in the capital, Obama will meet Widodo on June 30 and give a speech at an Indonesian diaspora convention the next day.
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