KLM will stop flying to Sudan from late March due to weak demand, an official of the Dutch airline said on Wednesday.
Lufthansa will be the last large European carrier to serve Khartoum apart from Turkish Airways.
Arab carriers also still fly to Sudan, which was once one of Africa's biggest growth markets, but their bookings have fallen, industry sources say.
KLM, part of Air France-KLM, will operate its three-times-a-week service from Amsterdam to Khartoum and Addis Ababa in Ethiopia for the last time on March 26, country manager Dick van Nieuwenhuyzen said.
The route has not been profitable since last year due to the exit of aid groups, he told reporters.
Until South Sudan's secession in 2011, foreign airlines enjoyed a bonanza as Sudan was flush with billions of dollars of oil revenues and Khartoum, the capital, hosted thousands of aid workers, UN officials and diplomats.
Such was the rise in traffic following the end of the civil war with the South in 2005 that Sudan planned a new airport to replace the current Khartoum International, built by British colonial rulers in the 1950s.
Authorities want to start construction this year but air traffic has dropped since the southern secession, which threw the economy into crisis with the loss of most oil reserves. The United Nations and aid groups have relocated most of their staff to South Sudan, while embassies have also cut staff.
Lufthansa threatened last year to halt its flights after Sudan tried to make it pay for jet fuel in dollars before backing off, the sources say.
The central bank forces foreign airlines to sell tickets in Sudanese pounds, which have more than halved in value since the southern secession and are nearly impossible to convert into dollars.