Rotavirus, which causes diarrhoea, and pneumococcal disease kill more than 2.7 million children worldwide each year.
The project is backed by the Global Alliance for Vaccines and Immunisation. At the launch health minister Alban Bagbin said the programme marked a “major fight-back”.
“Our children have been dying from these vaccine-preventable diseases for too long,” he said.
When combined with existing programmes against polio, measles and tuberculosis, Mr Bagbin said Ghana is on track to meet its target to cut childhood mortality by two-thirds by 2015.
The chief executive of the Global Alliance for Vaccines and Immunisation (Gavi), Dr Seth Berkley, told the BBC the combined treatment has become possible thanks to adequate health facilities in Ghana, combined with sufficient stocks of vaccine, and robust international funding.
Last year Gavi the secured supplies of the vaccines from major pharmaceutical companies at a large discount.
The organisation brings together the World Health Organisation, the UN’s children’s charity Unicef, the World Bank, vaccine companies and the charity set up by the Microsoft founder Bill Gates.