The men are part of the 19-strong Jordanian squad which has been training in Britain for the past two weeks.
Police in Antrim, Northern Ireland, said two of the men — aged 23 and 35 — face two counts of sexual activity with a child.
The younger man is also accused of voyeurism. He and the third man, aged 36, have been charged with sexually assaulting a woman.
The three were arrested before they were due to head to London for the start of the Games.
They are expected to appear at a magistrates court.
The men were held after complaints by staff at a leisure centre in Antrim, where they have been training, and two local women.
The Paralympic Games will take place Aug 29 to Sep 9.