Greater Manchester Police said the boy, who cannot be named for legal reasons, has been bailed with conditions not to attend any regulated football matches.
He is due to appear at Manchester and Salford Magistrates’ Youth Court on November 13.
The force added that a 14-year-old boy, who was voluntarily interviewed in connection with the incident, will be dealt with out of court.
Police launched an investigation into footage of chants at Manchester City’s home game against Brighton on Saturday.
City’s manager Pep Guardiola criticised the chanting, with the club also denouncing it as “vile”.
The chanting took place soon after the death of Manchester United and England great Sir Bobby was publicly announced.
Sir Bobby, a key member of England’s victorious 1966 World Cup team, died aged 86 on Saturday.