The FCDO initially warned of missile interventions in the vicinity of Aqaba's King Hussein International airport (AQJ) and seaport on Sunday (19 July).
However, several hours later, it upgraded its warning to advise against all but essential travel to both locations.
AQJ on Jordan's Red Sea coast is the country's second busiest airport after Queen Alia International in capital Amman.
The BBC reports two members of US military personnel were killed in an attack on a military base at the weekend. A third remains missing.
It is the latest flashpoint after a fragile ceasefire between the US and Iran collapsed a week ago, around a month after the two countries signed a memorandum of understanding designed to end the war in the region, which started on 28 February.
It comes amid amendments to the FCDO's advice for several other countries in the region, first for Bahrain and Kuwait, and latterly for the United Arab Emirates, Qatar, Saudi Arabia and Oman.
The FCDO advised against all but essential to travel to Jordan several days after the conflict in Iran started in February, which was lifted almost exactly three months later in early June. Operators, including Intrepid Travel and G Adventures, have either restarted their Jordan programmes, or pledged to.
The latest updates, while advising against travel to Aqaba airport and seaport specifically, do not extent to the rest of the country.
The FCDO advice issued on Sunday concerned "recent missile interceptions in the vicinity of Aqaba airport and seaport on 19 July".
Additional advice on regional tensions reads: "The US and Iran have announced a memorandum of understanding in relation to the conflict in the Middle East.
"The situation remains unpredictable. Iran has carried out further attacks on Jordan since the MOU was agreed, and could do so again at short notice."