A child, who is under the age of 13, was also allegedly sexually assaulted at the same site in Walthamstow, East London.
The two incidents are alleged to have taken place within weeks of each other at a hotel where 150 children are living alongside 250 adults.
It comes after growing concerns for the safety of refugees with fears of overcrowding and unsafe conditions.
Pressure is mounting on the home secretary Suella Braverman to look into the conditions of refugee centres.
The Metropolitan Police said that a man was charged on September 11 with one count of sexual touching of a child under 13 on September 9.
He has been bailed to appear at Stratford Magistrates’ Court on Wednesday November 9.
The force also confirmed the report of rape at the same hotel on October 5.
A spokesperson confirmed that a man in his 30s was arrested and taken into custody, he was bailed until January 2023.