Thousands were expected to pay their respects at the theater, which planned to let them in 600 at a time to listen to his music, watch a video tribute and leave flowers and memorabilia.
The event was set to start at 2 p.m., but many people were already waiting Tuesday morning, dancing as they lined up with T-shirts, posters, album covers and other mementos.
Fans began converging on the Apollo as soon as Jackson died Thursday in Los Angeles, and it has continued to serve as an impromptu memorial site in the days since.
The pop icon's ties to the theater go back to 1967, when The Jackson 5 won the Apollo's Amateur Night contest. The appearance is credited with helping to launch the brother act's career, which later propelled Jackson to solo stardom.
He last appeared at the Apollo in 2002, invited by former President Bill Clinton for a Democratic National Committee fundraiser.
Tuesday's salute was to begin with a eulogy by the Rev. Al Sharpton. A moment of silence was planned for 5:26 p.m., the time East Coast fans learned that Jackson had died.
Outside the theater, fans could write messages on a wall outside on 125th Street in the center of Harlem.
The Apollo also played a role in remembrances for James Brown after his death in 2006, hosting a public viewing of the "Godfather of Soul" for thousands of fans.
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