Mr Kenyatta on Friday urged the US to respect the will of the Kenyan society, which he said had rejected same-sex marriages.
“We share a lot of things but gay issues are not among them… We cannot impose on people what they don’t accept,” Mr Kenyatta said during a joint press conference at State House, Nairobi.
At the moment, Mr Kenyatta said, Kenya has trained its eyes on boosting trade, health, democracy, security, women and youth empowerment, not gay rights.
“The health issues we have discussed are critical. Once we are done with that, we can then focus on those other issues,” he said.
Earlier, President Obama had emphasized the need for Kenya to stop discriminating against gays and lesbians, saying all people, including homosexuals, should be treated equally under the law.
“When a government starts treating people differently, that habit starts to spread,” he said, adding that segregating people based on their sexual orientation “erodes freedoms.”
“If somebody is a law abiding citizen who is going about their businesses, working in their jobs, obeying the traffic signs and doing the other things that good citizens do and not harming anybody, the idea that they are going to be treated differently or abused because of who they love is wrong ” he stated.
The US leader is in Nairobi for the Global Entrepreneurship Summit that kicked off on Friday.
Before his arrival in his father’s homeland, Kenyan leaders, led by Deputy President William Ruto, had urged Mr Obama not to discuss gay rights on his visit.
Hundreds of protestors also took to the streets of Nairobi in an anti-gay march attended by politicians, church leaders and civil society members.
Their request was, however, dismissed when the White House announced that Mr Obama was free to speak on anything he wished.
While homosexuality is illegal in Kenya, gays and lesbians have been coming out of the closet and declaring their sexual orientation openly.
This is not the case in some African countries, like Uganda, where gays and lesbians have been attacked and even killed.