Her shoulder injury required simple surgery. In blockaded Yemen, that was out of reach. And so Manal’s right arm shrank as her left arm grew stronger, and her father started to turn away when she was being bathed or dressed. “I couldn’t stand the sight of her,” Abdullah Ali Lutfallah said. “It broke my heart.”

After a year and a half of negotiations, five-year-old Manal was among eight children to be evacuated from Sana’a this week for medical treatment in Jordan on the first civilian flight permitted to leave the Yemeni capital in three years. A second aircraft carrying an additional 24 patients was scheduled to leave for Amman on Friday, with a third bound for Egypt expected to follow soon.

The “mercy flights” are a rare humanitarian breakthrough in a stagnating five-year conflict between parties used to dealing in the zero-sum logic of war. Even the night before the first aircraft took off on Monday, the Houthis who control most of northern Yemen, including Sana’a, threatened to withdraw permission. Yemen’s internationally recognised government, which enforces a strict air-and-sea blockade on rebel-held territory, also held up the process at earlier stages.

Facebook Twitter Pinterest Yemeni patients boarding their UN-sponsored flight in Sana’a on Monday to travel for medical treatment in Jordan. Photograph: Mohammed Hamoud/Getty Images

“On at least four occasions, a hard-fought consensus broke down and every time that happened, people who should have been receiving care died,” a person familiar with the matter said. “It was deeply frustrating for everyone working on the issue because we all knew how many lives were at stake, and the people who needed help the most were the ones being sacrificed.”

For the past three months, a hotel in Sana’a became a makeshift waiting room for about 30 families, some trying to keep their children alive long enough for Yemen’s duelling governments to agree to allow them to go abroad for treatment.

The Houthi health ministry says 32,000 people in the territory it holds are unable to receive proper medical care due to the blockade, which has been blamed for exacerbating a humanitarian crisis that has displaced 4.3 million people and left 80% of the population without enough food, safe water or sanitation.

“I didn’t believe it was really happening until the plane took off,” said Majdi Abdulwahab, whose daughter Samira, 10, underwent reconstructive ear surgery at Amman’s Speciality hospital on Wednesday morning, five years after being injured in a motorcycle accident.

Even before the war, Yemen’s health system was one of the least developed in the region. Once the fighting started, cases such as Manal’s traumatic shoulder injury became impossible to treat. “I submitted her case to a rehabilitation centre and after three months they told us they couldn’t help her,” Lutfallah, 40, said. “We took her back to the doctor, and he said he couldn’t help her either.”

Facebook Twitter Pinterest Ayman in his hospital bed in Jordan after being airlifted from Yemen. Photograph: Asmahan Bkerat/The Guardian

Wahib Senan took his son, Ayman, 10, to several doctors and lobbied high officials to find treatment for the scoliosis that started curving the boy’s spine four years ago. “They always told us he had to fly abroad,” he said. “He couldn’t sleep or live his life normally … Seeing your son dying is crushing.”

Getting registered on a list of patients eligible to be flown overseas was the start of a torrid new chapter. Flights were regularly scheduled then cancelled after negotiations broke down. “We would only be told, the flight was cancelled,” Senan, 40, says. “[Ayman’s] mother started telling me to quit, that we would never get it.”

Behind the scenes, international officials worked to build consensus between the parties involved. “For two years, every time there was a breakthrough, one of several of the parties backtracked from their commitment,” a source familiar with the process said.

The logistics presented another set of hurdles, including finding airlines willing to take out war insurance to conduct the flight, and finding a UN plane that might be free amid a global scramble to evacuate citizens from coronavirus-hit China.

Nursing his daughter in a hotel room, Abdulwahab said he struggled to understand why getting a 10-year-old girl into surgery was so fraught: “What is the fault of those who are suffering from sickness to be dragged into the politics of the world?”

For instance, in October, dozens of families with sick children were summoned to Sana’a and told to prepare to fly. A few days later, they were informed that negotiations had broken down and the airlift was cancelled. “We were devastated,” Abdalwahab said.

Over the next weeks, new flights were repeatedly scheduled then cancelled at the last minute. International officials were reluctant to send the families home, and by that point, Senan said, he would not have left anyway. “I was either going to get my son treated or die with him,” he said.

“You cannot imagine what it was like, psychologically, for those waiting at that hotel,” said Lutfallah. “One woman had cancer, and because she couldn’t get medical care in time, she lost her eyesight. Another father of a young girl was told that they would have to amputate both her legs, but he refused, because he knew she wouldn’t get proper care in Yemen.”

For two children, Khalid and Abdullah, authorities agreed to the flight too late – and just in time. Khalid, 9, had entered the first stage of renal failure. “Without dialysis, his kidney would have totally failed,” said Ashraf Shami, a paediatrician overseeing his case in Jordan.

Abdullah, 13, had found a donor in Yemen to give him a healthy kidney, but no place there to perform the surgery. The pair were onboard the first flight to Jordan on Monday. “He had months to live,” Shami said. “Maybe less.”

Additional reporting by Jassar Al-Tahat