Between 100 and 150 troops had been sent after the agreement was signed between the two countries at the start of this year, military spokesman Brigadier Richard Karemire told The Associated Press.
The government of Equatorial Guinea hopes the "training and monitoring" team from Uganda will work toward reaching "a certain level of professionalism" among the Guinean armed forces. The Ugandans will be stationed in the West African country for at least a year but could stay longer, he said.
Uganda and oil-rich Equatorial Guinea are led by two of the world's longest-ruling presidents, and both men face charges of dictatorial rule. Equatorial Guinea is also where former Gambian dictator Yahya Jammeh fled into exile in January after ruling his country for 22 years.
Over the years, Ugandan troops have been deployed in many parts of Africa, leading to charges of military adventurism against Ugandan President Yoweri Museveni, who has held power for three decades.
Ugandan troops have been deployed to Central African Republic, Congo, South Sudan and Somalia, where they part of an African Union peacekeeping force defending the government against Islamic extremist rebels.