The advisory is likely to impact air travel to and through the region amid the heightened tensions between the United States and Iran.
The advisory warned all commercial aircraft flying over the Gulf region of "heightened military activities and increased political tensions”, which "present an increasing inadvertent risk to US civil aviation operations due to the potential for miscalculation or misidentification”.
The FAA also said that the aircraft flying in the area could encounter "inadvertent GPS interference and communications jamming” that "could occur with little to no warning”.
The latest advisory brought back memories of a deadly incident, when the US Navy accidentally shot down an Iran Air passenger plane at the height of the Iran-Iraq war in 1988. The jetliner, which was flying from Tehran to Dubai, was mistaken for an Iranian F-14 jet fighter.
Two missiles fired at the plane from the USS Vincennes killed all 290 people on board.
Two weeks ago, Washington deployed an aircraft carrier group and B-52 bombers to the Persian Gulf against, what it claims, is an imminent threat from arch-foe, Iran. US President Donald Trump has also ordered nonessential diplomatic staff out of Iraq, citing threats from Iranian-backed Iraqi armed groups.
Last weekend, Tehran was blamed for sabotage attacks on four Saudi oil tankers off the coast of the United Arab Emirates (UAE). But Iran said Washington was engaging in psychological warfare before warning it could easily hit US ships too.
Stepping up the rhetoric, a deputy from Iran's Revolutionary Guard has said that any armed conflict with the US would affect the global energy market. Iran has long threatened to shut off the nearby Strait of Hormuz, through which a third of all oil traded at sea passes.
The region has become a vital connection point for the global aviation industry. Dubai International Airport in the UAE is the world's busiest for international travel. Popular long-haul carriers Emirates, Etihad and Qatar Airways operate from Gulf air hubs.
As well as the risk to airlines, insurer Lloyd's of London has warned of increasing risks to maritime shipping in the region from the tensions.
The latest tensions all take root in Trump's decision last year to withdraw from the 2015 nuclear accord between Iran and world powers and impose wide-reaching sanctions. Iran recently gave Europe a 60-day deadline to come up with new terms, or it would begin enriching uranium closer to weapons-grade levels.
Earlier this week, EU foreign affairs chief Federica Mogherini – after a meeting with US Secretary of State Mike Pompeo – said the EU member states continued "to fully support the nuclear deal with Iran”.
German Foreign Minister Heiko Maas said he had again told Pompeo that Berlin did not want a military escalation. He also stressed that in Europe's view, the pact was the best way to prevent Iran from building an atomic bomb.
British Foreign Secretary Jeremy Hunt said the UK was worried about the risk of accidental conflict between Iran and the US.