Andrew and Liz Buxton, from the Leith Valley Presbyterian Church, an engineer and an architect, were in South Sudan on mission work when ethnic violence erupted during the middle of last month.
In an email to supporters on Saturday, they said they had been caught up in the fighting while working in Malakal, a city near the border with Sudan, about two weeks ago.
Armed forces in the city began dividing into pro and anti-government factions and fighting each other, and Malakal airport was closed 45 minutes before a flight was due to land that would have carried them to safety, they said.
The couple spent three days ''hiding in our compound as war raged in Malakal'', before the situation began to stabilise from December 27, they said.
That allowed them to seek refuge in a United Nations compound in Malakal, along with 25,000 others displaced by the fighting in the city.
They remained in the compound for three nights before boarding a flight to the Kenyan capital, Nairobi.
The couple said it was ''hard to describe what we went through in a few words'', but the fighting in Malakal alone was believed to have claimed the lives of more than 2000 people and 60% of the city's shops had been looted.
That raised the prospect of a food shortage, and the couple were urging their supporters to pray for the country as it faced an ''uncertain'' future.
The couple have worked for Serving in Mission, an international Christian mission organisation, in South Sudan periodically since 2008. information on Mr Buxton's LinkedIn page showed.
Mr Buxton was appointed deputy director of Serving in Mission's 50-strong South Sudan team last February.
Serving in Mission had since evacuated all its staff from the country, at least for now, creating a sense of frustration for some, ''especially after many left South Sudan without being able to say proper farewells'', the couple said.
''Hearing stories from friends tears at our hearts and in one sense makes us wish we were still there to try and help in small ways that we could,'' they said.
Official estimates put the death toll from the violence at more than 1000, while media reports said another 120,000 people had been displaced as the violence spread.
