The president said that the two countries would stay close to ensure "economic growth and financial stability".
He said the UK and EU were still "indispensable partners" for the US.
The UK's decision to leave the EU had raised questions about its relationship with the US, a long-time ally.
"While the UK's relationship with the EU will change, one thing that will not change is special relationship that exists between our two nations," Mr Obama said.
The president said he was confident that the UK was committed to an orderly transition from the EU.
During a visit to the UK in April Mr Obama urged Britons to vote to stay in the EU.
He warned that a Brexit would put the UK at "the back of the queue" for negotiating a trade deal with the US, which is focused on striking a free trade deal with the EU.
Mr Obama said he valued his relationship with David Cameron, who said today he would step down as prime minister by October. The two men will have been in office for nearly the same period of time.
The president was speaking at Stanford University on Friday at an entrepreneur summit.
"Yesterday's vote speaks to the ongoing changes and challenges that are raised by globalisation," he told the audience.
Barack Obama said that the special relationship between the US and the UK would endure despite Britain's decision to leave the European Union.