The organisation said it would use the sum to hire 15 specialists to help victims and those at risk of child sex exploitation.
A report last year said around 1,400 children had been sexually exploited in Rotherham between 1997 and 2013.
Funded by the Government, Rotherham Council and the KPMG Foundation, the three-year programme will look to raise awareness about the crime, by working closely with schools and local communities.
Professionals will also be trained to enable them to spot the signs of sexual exploitation early.
Javed Khan, chief executive of Barnardo's, said: "We are intent on tackling this horrendous crime and supporting victims as they try to rebuild their shattered lives.
"This partnership signals a new era as far as confronting child sexual exploitation in Rotherham.
"Barnardo's is really proud to be a part of the team that will contribute to eradicating this horrific crime."
He added: "We must all be alert to spotting the signs that sexual exploitation may be taking place. It is everyone's responsibility to protect those children who are most vulnerable from ruthless predators."
Barnardo's said it derives its inspiration and values from the Christian faith.
"These values, enriched and shared by many people of other faiths and of no religious faith, provide the basis of our work with children and young people, their families and communities," it said.