Netanyahu, welcomed at the airport by Rwandan President Paul Kagame, later visited the Kigali Memorial Centre, where more than 250,000 victims of the at least 800,000 victims of the 1994 genocide are buried in mass graves.
"The Rwandan government felt a real affinity with Israel for obvious historic reasons," said Phil Clark, a Rwanda specialist at London's SOAS university.
"Israel was seen as a small country in a very hostile neighborhood; a country with very few resources but which had recovered from its genocide very quickly and very impressively," Clark said. "So Israel was an obvious place for Rwanda to look to for inspiration."
In 2014, when Rwanda sat on the UN Security Council, Kigali abstained from a resolution -- ultimately rejected -- advocating the end of the occupation of Palestinian territories.
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Netanyahu's visit to Rwanda is part of a four-nation Africa trade and security tour aimed at boosting ties.
On the eve of Netanyahu's tour Israel announced a relatively modest USD 13 million aid package to strengthen economic ties and cooperation with African countries.
It also sees African countries as potential allies, particularly at the United Nations and other international bodies, where it is regularly condemned over its occupation of the West Bank and blockade of the Gaza Strip.
On Monday, Netanyahu visited Uganda to commemorate the 40th anniversary of the Israeli raid on Entebbe airport in which his brother Yonatan was killed rescuing hostages held by German and Palestinian hijackers.
Yesterday, he visited Kenya, and will end his tour on tomorrow in Ethiopia.