The Uganda government has secured 2,100 doses of an Ebola vaccine for the exercise.
Addressing journalists in Kampala on Friday, Uganda’s Health Minister, Dr Jane Ruth Aceng said 40 health centres have been identified for the vaccination exercise.
With the introduction of the vaccine Uganda is to become the first country in the world to provide a vaccine against Ebola without experiencing an active outbreak.
The country’s health authorities along with the World Health Organization have taken the decision after the threat of the spread of Ebola from neighboring DRC Congo.
The Ebola outbreak in eastern DR Congo has claimed 170 lives.
WHO has warned that the risk of Ebola spreading from the DRC to other countries is "very high" due to ongoing violence from militia groups, as well as the outbreak's proximity to the neighboring countries of Uganda, Rwanda and South Sudan.
Dr Yonas Tegegn, the WHO country representative for Uganda says the recombinant vesicular stomatitis virus–Zaire Ebola virus (rVSV-ZEBOV) has been proven to have a higher efficacy rate.
Vaccination teams have been deployed in the west, close to the border, to start work in the five most-at-risk districts.
The vaccine to be used in Uganda is the same one that helped contain the Ebola outbreak in West Africa and is currently being used to control the disease in eastern DR Congo.
Uganda has already been taking other measures such as the screening of people crossing at some border points.
Ebola is a severe illness with a fatality rate of up to 90 percent and considered one of the world's most virulent diseases.