The "QOM-1" drone came within 100 feet below the aircraft and 200 feet to the side of the aircraft. The F/A-18 was in a landing pattern several thousand feet off the deck of the ship waiting to land.
The F/A-18 maneuvered repeatedly to avoid the drone officials said and it did not appear to be armed.
The officials said the drone encounter was considered "unsafe and unprofessional."
The US used an emergency radio frequency in the immediate area to warn those operating the drone to back away. It did eventually move off.
US Naval Forces Central Command issued a statement later Tuesday confirming the incident.
It said the US jet "had an unsafe and unprofessional interaction with an Iranian QOM-1 unmanned aerial vehicle," adding that "despite repeated radio calls to stay clear of active fixed-wing flight operations," the Iranian drone "executed unsafe and unprofessional altitude changes in the close vicinity of an F/A-18E."
"The dangerous maneuver by the QOM-1 in the known vicinity of fixed wing flight operations and at coincident altitude with operating aircraft created a collision hazard and is not in keeping with international maritime customs and laws," the statement said.
The Navy said this was the thirteenth such "interaction between US and Iranian maritime forces in 2017."
Pentagon spokesman US Navy Capt. Jeff Davis previously told reporters that there had been 35 incidents of such behavior by Iranian vessels in 2016.
This is not the first time the US Navy has accused Iranian drones of operating unprofessionally while in close proximity to US ships.
In January 2016 an Iranian drone flew over the French aircraft carrier Charles de Gaulle and the USS Harry S. Truman, both of which were operating in international waters in the Gulf at the time.
A Navy helicopter was launched from the Truman in response and it determined that the Iranian drone was not armed.
The US Navy described that incident
as "abnormal and unsafe" and it took place the same day that Iran seized 10 American sailors whose boats had strayed into Iranian waters.
Tuesday's incident comes on the heels of another encounter between US and Iranian ships late last month.
The USS Thunderbolt fired warning shots at an armed Iranian patrol boat in the northern end of the Persian Gulf after the Iranian Revolutionary Guard Corps, according to a defense official familiar with details of the incident. The officials said the Iranian boat approached and came within 150 yards of the USS Thunderbolt, a US Navy patrol ship.