The visit has seen the United States increase its security assistance to Kenya, although Obama also urged the country to respect its Muslim minority.
The Kasarani stadium complex where he delivered the speech was used to hold hundreds of ethnic Somalis during controversial mass arrests following the 2013 Somali-led Shabaab assault on the Westgate shopping mall in central Nairobi that killed 67.
Obama then headed to meet members of Kenya’s vibrant civil society — bearing the brunt of what they say are increased restrictions as Kenya fights its own “war on terror” – and will give an interview with prominent Kenyan broadcaster Capital FM.
Obama’s visit to Kenya had been delayed while President Uhuru Kenyatta faced charges of crimes against humanity for his role in post-election violence seven years ago.
The International Criminal Court has since dropped the case, citing a lack of evidence and accusing Kenya of bribing or intimidating witnesses, although the trial of deputy president William Ruto continues.
On Saturday, Obama also stressed the importance of protecting basic rights, comparing homophobia in Africa to racial discrimination he had encountered in the United States.
“As an African-American in the United States I am painfully aware of what happens when people are treated differently under the law. I am unequivocal on this,” Obama said, openly disagreeing with Kenyatta.
Homophobia is on the rise in Africa, and espousing evangelical Christian values is a major vote-winner in many countries. Kenyatta replied by repeating the view that gay rights were unacceptable to Kenyans and therefore “a non-issue”.
Obama leaves later Sunday for the Ethiopian capital Addis Ababa, where he will also become the first US leader to address the African Union.
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