They have pledged to work together to fight terrorism and improve healthcare.
The US President has been discussing a range of issues during his first visit as president to Kenya, his father’s homeland.
But the US and Kenyan leaders disagreed on some matters, including the country’s record on gay rights.
Obama called for an end to discrimination and more efforts in the fight against corruption.
He also pledged more support for women and girls.
“We’re working together to ensure that girls have access to education and that women are protected from violence,” said Obama.
“Today I can announce that Kenya will be part of our ‘Dreams’ initiative, to help keep adolescent girls safe and AIDS free.
“And across Africa, Kenya and the United States will keep working to strengthen public health systems and deal with outbreaks and diseases before they become epidemics”.
Obama also laid a wreath in memory of the victims of the 1998 bombing of the US Embassy in Nairobi by Islamist militants.
A total of 213 people died in the blast.
The site of the attack is now a memorial park.