The agreement which was signed by Mr Alex Segbefia, Minister of Health on behalf of Government and Dr Mark Dybul, Executive Director of the Fund, was witnessed by President John Dramani Mahama.
The Fund would be used for the next three years in the fight against the three diseases.
President Mahama said government would step up the fight against the incidence of malaria and help reduce the pressure on the National Health Insurance Scheme.
He said over the years, malaria accounted for almost half of the total cases recorded at various out-patient departments in the health facilities.
He said a high level education coupled with the further distribution of 19 million insecticides treated mosquito nets would lead to significant reduction of the disease.
He said 76,500 tuberculosis cases that have been detected and gave the assurance that the money would be used judiciously to meet all the health development goals.
President Mahama said the Ministry of Health, Ghana Health Service (GHS) and other stakeholders would scale up educational programmes on the three diseases to ensure its elimination or drastic reduction in the coming years.
He said there has been tremendous improvement in the prevention rate and elimination of the mother-to child HIV transmission from 50 to 62 per cent and would continue to ensure that figures are increased annually.
Dr Dybul commended President Mahama for the reduction of malaria, tuberculosis and HIV and AIDs cases and gave the assurance that they would continue to work with government to achieve their goals.
He said Ghana has over the years recorded 60 per cent reduction in the incidence of malaria and they would continue to support the nation to achieve her health targets.
On HIV and AIDS, the Executive Director said Ghana had also excelled in the distribution of the Anti-Retroviral drugs to many patients thereby creating comfortable conditions in the country.
Dr Magda Robalo, Country Representative of the World Health Organisation (WHO), commended the GHS and government in general for their commitment in fighting the diseases.
She said her office would continue to support Ghana to achieve her health development goals when she takes the new position in-charge of the WHO Communicable Diseases in the Region.
Mr Collins Agyarko-Nti, a Representative of the Country Coordinating Mechanism, gave the assurance that they would continue to mobilize funding for government to achieve goals.