Netanyahu is also scheduled to visit Kenya, Ethiopia and Rwanda.
An El Al Israel Airlines plane carrying Netanyahu and his wife landed at Entebbe International Airport at exactly 1.40pm (12:40 Rwandan time), and was welcomed by Ugandan President Yoweri Kaguta Museveni and his wife Janet Museveni.
Israel's warm ties with Africa were sullied by the 1967 and 1973 wars against its Arab neighbours, the 1976 raid on Entebbe, and cooperation with the apartheid regime in South Africa, which Jerusalem helped develop nuclear technology and other commercial ties despite a boycott by many countries in the world.
In Uganda, Netanyahu held a summit with leaders of seven African nations in the region aimed at strengthen ties, with Israel providing them with its expertise in security and technology, while receiving in exchange support from new friends that will refrain from criticizing Israeli policies and also provide diplomatic backing in worldwide forums. "This will have an impact in Africa now, but I think that it will have very considerable effect regarding Israel's global relations in the future, vis-à-vis our effort to bring about a very great number of countries that support Israel", he said. The State of Israel has changed that.
An Israeli band played somber tunes at the airport on the shore of Lake Victoria, to mark the anniversary of the Israeli rescue mission, during which three hostages were killed. "We are eager to work with you by learning from capacities we have strongly built in different sectors", Netanyahu said. Yonatan Netanyahu, the only Israeli commando killed, has become a symbol of bravery in his country. Israel would also provide African states with training in "domestic security" and health, it added.
The effort comes as Israel's ties with some of its long-time allies such as the United States and European Union have come under strain recently. His death made Yonatan an Israeli hero, and thrust Netanyahu toward public life.
The occasion marked the first official visit of an Israeli premier to sub-Saharan Africa in 30 years.
He later takes part in an anti-terrorism summit alongside leaders from Ethiopia, Kenya, Malawi, Rwanda, South Sudan and Zambia, before heading to Nairobi later on Monday. The Palestinians have used their upgraded status to launch a diplomatic offensive against Israel and its occupation of lands where the Palestinians hope to establish a future state. Mr Netanyahu visited the airport a few years ago when he was out of government.
Beyond diplomacy and trade, the trip has deep personal meaning for Netanyahu. The Ugandan president at the time, Idi Amin, openly supported the hijackers demanding the release of Palestinian militants in Israeli prisons and prisoners in other countries.