He reassured Arab leaders, after a two-day summit, that the US was committed to protecting them in a time of "extraordinary changes".
Speaking at Camp David near Washington, Mr Obama said a nuclear deal with Iran was not a threat to Gulf nations.
A joint statement pledged new co-operation in many areas.
These included counterterrorism, maritime security, cyber-security and ballistic missile defence.
The six-nation Gulf Co-operation Council (GCC) is made up of Bahrain, Kuwait, Oman, Qatar, Saudi Arabia and UAE.
"I was very explicit ... that the United States will stand by our GCC partners against external attack,'' Mr Obama pledged at the end of the talks.
The president said he hoped that working together would help achieve "the kind of peace and good neighbourliness with Iran" that the nations present sought.
