The lucky ones heard the first explosions and hobbled or were carried by doctors and nurses to one of the hospital bunkers.
The less fortunate patients, some wounded and too feeble to move, along with the doctors and nurses who were treating them, had no time.
"The patients who were unable to escape burned to death as they lay in their beds," said Heman Nagarathnam, the head of programs for Doctors Without Borders in northern Afghanistan.
Over the next hour, witnesses said, what unfolded was a relentless air assault that put patients, doctors and the Kunduz hospital operated by Doctors Without Borders with no possibility of escape.
The bombing began at 2.08am (local time) and continued until 3.15am, Mr Nagarathnam said. "The bombs hit and then we heard the plane circle around," he added. "There was a pause, and then more bombs hit.
“The main hospital building was engulfed in flames,” he said.
For Najeebullah (38) a resident of Kunduz City, the bombing seemed part of a nightmare that would not end.
It had started two days earlier when he attempted to move his family of five children, ages 3 to 12, and his brother-in-law and sister-in-law from one side of the city to the other.
An aircraft, apparently targeting some Taliban forces nearby, hit his vehicle. His 9-year-old son, Muheeb-ul-Rahman, and his 7-year-old son, Fawad, were killed instantly, his three other children were wounded and he took them to the Doctors Without Borders hospital.
Two of his children were discharged, but his son Waheedullah (4), had abdominal wounds as well as back injuries so Najeebullah stayed with him in a makeshift shipping container the hospital was using for the overflow of patients wounded in the fighting in Kunduz, which by Friday had been going on for five days.
As he sat near his son who was being examined by medical staff, “there was a horrifying sound, then a massive explosion, that turned everyone fearful,” he said.
“A war jet targeted the building close to us where the doctors perform surgeries. Everyone ran here and there without even knowing where they were going.”
After the first blast, some 20 more followed, he said. “Everyone believed it was his last day on earth. There was blood and bodies scattered everywhere. Many of them were doctors, Afghans, whom I had seen in my last two days at the hospital.”
Of the 19 killed in the attacks, 12 were hospital staff members, among them four Afghan doctors, according to eyewitnesses.
One of the slain, Dr Ehsan Usmani, seemed to have sensed things were getting worse, and on Friday evening posted a desperate message on his Facebook page, cursing Afghanistan's leaders for allowing the security situation to deteriorate into a war.
"A thousand curses on you Ashraf Ghani and Stanekzai that you bloodied and covered in dust the people of Kunduz with your blind bombings," he wrote, referring to the Afghan president and Mohammad Masoom Stanekzai, the minister of defense.
The Afghan military has also been using helicopter airstrikes to target the Taliban, but sometimes misses and hits civilians.
"Spit, spit, spit, spit on your faces," Dr Usmani wrote and then, more desperately: "Hey people, share this message that since this afternoon the bombers of the dirty and unclean government have been killing, maiming and wounding the innocent people of Kunduz."
Eight hours later, he was dead, according to colleagues at Doctors Without Borders.
The personnel who survived tried to help those wounded in the bombing, and set up a makeshift operating theater. Some patients were transferred to the regional hospital, others to a neighboring provincial hospital.
By nightfall, though, there were hardly any medical workers left at the regional hospital; they had fled in fear.
"The entire system has broken," said Saad Mukhtar, director of public health for Kunduz Province. "Everyone tries to save himself or herself."
Mr Mukhtar said medicines were on the way, but added, “Who can use them, when there is no system, no doctors, no nurses, what even can we do when the medicines get there?
“There has been a tragedy, even worse than a tragedy, in Kunduz.”
New York Times