The three "enemy combatants" are aged between 13 and 15 years old and were the youngest of the 660 suspected Taliban and al-Qaida members being held without charge at the US naval base on Cuba.
Never tried or officially charged, the boys' detention had drawn severe criticism from human rights groups before they were handed over to the International Committee of the Red Cross last Thursday.
The Red Cross also organised transport to Afghanistan for the teenagers so they could rejoin their families – the first time the boys will have seen their parents since the end of 2001.
They were captured in Afghanistan by the US military on suspicion of supporting the Taliban – who were toppled in 2001 for harbouring Usama bin Ladin and his al-Qaida network.
'Allowed to play'
"They were in good form," General Baba Khan, Kabul's police chief, told journalists.
"I saw them. They said they were kept in separate cells from the elderly inmates and were allowed to play and have fun."
The US has told Afghan authorities not to release the boys' names "for fear of reprisals against them".
The American military has already freed more than two dozen Afghans from Guantanamo. Many have complained about ill treatment during their detention.
More than 650 captives remain at the prison camp in Guantanamo with no access to lawyers, nor with dates either for trial or release.