The incident happened Tuesday and involved the USS Thunderbolt, a Cyclone-class patrol ship involved in an exercise with American and other vessels in the Gulf.
Iran unveiled its latest air defence missiles on Saturday.
That wasn't the case in January, when the Mahan fired warning shots after five Iranian vessels approached the destroyer and two other USA entering the Strait of Hormuz.
It is not clear where in the Persian Gulf the incident occurred or how many Americans were aboard the Thunderbolt.
The Navy characterized the Iranian boat's actions as not following internationally recognized "rules of the road ... creating a risk for collision".
In reply the IRGC third naval zone said that its forces neutralized the USA vessel's provocative move.
According to the USA statement, the Iranian boat approached the USS Thunderbolt, coming within 137 meters (150 yards).
The vessel from Iran's Islamic Revolutionary Guard Corps (IRGC) "conducted an unsafe and unprofessional interaction" with the coastal patrol ship USS Thunderbolt as it participated in a military exercise in the worldwide waters of the northern Arabian Gulf.
Back in June, the USA claimed an Iranian boat aimed a laser on a US helicopter accompanying a formation of American ships in the Strait of Hormuz, at the mouth of the Persian Gulf.
Of the incidents at sea a year ago, the worst involved Iranian forces capturing 10 US sailors and holding them overnight.
The shots were used as a last resort after the Iranian ship failed to respond to calls over the radio and sound signals from the American ships, including five blasts from the U.S. Navy ship's whistle, an worldwide symbol for danger.
Hostility between the United States and Iran date back to the 1979 Islamic revolution, which overthrew the USA -backed monarchy in Tehran.
The boats had been on their way from Kuwait to Bahrain and experienced engine trouble, according to the U.S. Navy.