The summit, to be held in the capital, Nairobi, from 26-28 July, could provide “a target for terrorists”, the US State Department said in a statement.
In 2013, at least 67 people died in an attack by al-Shabab militants on the Westgate shop centre in Nairobi.
The Somali-based Islamist militant group says it is at war with Kenya.
In April, al-Shabab killed 148 people, mainly students, in an attack on Garissa University College in the country’s north-east.
The US State Department has urged its citizens to “maintain a high level of security awareness” as part of the new travel warning, which expires on 30 July.
Mr Obama’s visit to Kenya will be his first to his father’s homeland as US leader.