"A gallon of petrol now costs 25,000 pounds (around $42) on the black market," bus driver Baraa Abdellatif told AFP at one filling station. That price was more than eight times what it was before Sudan's rival generals began their war on April 15.
At other stations the price could be even higher. The Norwegian Refugee Council cited up to 40,000 pounds a gallon (4.5 litres).
The queue had left Abdelrahman Hussein waiting by his car "for 48 hours" under the blazing sun.
"I'm trying to join my family in Sennar", 100 kilometers further down the road, he said.
Shaul Myke fled years ago from war-ravaged South Sudan looking for peace in Khartoum. Now she is on the run again - six children in tow - after Sudan's capital became a battle zone.
But with fuel in short supply and ticket prices escalating, she is stuck.
Myke and her youngsters "have been waiting under the sun for four days", she told AFP on the side of a road southeast of Khartoum.
At the entrance to Wad Madani, 200 kilometres (124 miles) from the Sudanese capital, she and dozens of other South Sudanese watch the few cars that pass.
They cannot find a way south.
Soaring fuel prices - and an exodus of residents desperate to escape the violence -- have pushed bus ticket prices up as well.
A United Nations report on Monday cited "reports of rapidly rising transport costs, making it increasingly difficult for people to leave conflict-affected areas. Cash is scarce and hard to access."
"I just need to find a way south to Kosti," the last major town before the South Sudanese border, Myke said. Her children and what luggage she could carry out of the city were scattered around her.
Like Myke, many of the 800,000 South Sudanese refugees in Sudan have been forced to turn back towards the south, in fear of the fighting which has claimed at least 459 lives, according to the UN.
Driven by the same despair, Fawzia Abdelrahim took her family of five to Wad Madani, where she knew no one.
"We don't have any relatives here, but fortunately the neighborhood residents opened up a school for us," she told AFP.
Ten families, including that of Al-Amin Mohammed, now spend the night in the school.
"Even sleeping on the ground, we're much better off than the days of terror we lived through," he said.