The Brit was deemed a fugitive by Brazilian police after he absconded from the Copacabana Palace hotel when the authorities attempted to re-arrest the businessman last week.
Whelan was initially taken into custody regarding allegations of bribery, money laundering and tax evasion in relation to a World Cup ticket scam.
According to The Guardian, a court spokeswoman confirmed yesterday that Whelan has now handed himself in to the Rio de Janeiro state Justice Tribunal and will be picked up by police.
Before Whelan's arrest, 11 other people were taken in by the authorities in connection with the alleged scam.
Whelan's company was a FIFA partner for the tournament.