Young Palestinian militants shouted into walkie-talkies as they loaded anti-tank obstacles into a pickup truck, an AFP correspondent reported as he toured the camp after the troops left.
Black canvas sheets littered the narrow alleyways of the impoverished camp, torn down after providing cover from Israeli drones.
Damaged parts from Israeli armoured vehicles were laid out on a main street, adorned with the flag of the Palestinian militant group Islamic Jihad.
The Palestinian health ministry in Ramallah said Israeli forces had killed 12 people including four children, and wounded 25 during the fighting which began on Tuesday morning.
The bodies of several people killed in the clashes were wrapped in black and green flags and placed on stretchers which were then hoisted on the shoulders of supporters.
They were carried through the streets of downtown Jenin on Thursday, surrounded by armed militants from Islamic Jihad, who chanted "Allahu akbar" (God is greatest) and fired automatic weapons into the air in salute.
The body of local surgeon Usaeed Jabareen received a special commemoration from staff at the government hospital in the city.
Crowds lined a courtyard and stairwell, before holding a memorial for him in the courtyard outside. 'We live in misery'
Jenin has long been a stronghold of Palestinian militant groups and the Israeli army routinely carries out raids in the city and the adjacent camp.
This time, Israeli forces stayed in the camp for about two days.
Troops took over a two-storey sports centre, where foam mattresses were strewn around and chairs arranged in circles.
Dozens of McDonald's wrappers were littered across a weights room and some of the exercise equipment had been defaced.
The West Bank, which Israel has occupied since 1967, has experienced a surge in violence for more than a year, but especially since the Israel-Hamas war erupted on October 7.
At least 518 Palestinians have been killed in the territory by Israeli troops or settlers since the Gaza war broke out, according to Palestinian officials.
Attacks by Palestinians have killed at least 12 Israelis in the West Bank over the same period, according to an AFP tally of Israeli official figures.
The army said it had raided the house of Ahmed Barakat, who was suspected of involvement in an attack on an Israeli civilian last year.
Barakat's house was reduced to rubble in the operation.
After the troops left, children played outside.
"I was afraid when the Israeli army came here," said a young boy, as he kicked a football.
AFP journalists on Thursday morning saw dozens of recently damaged buildings in the camp.
Some of the structures had been completely destroyed, while others were less severely damaged.
On the roof of one of the damaged buildings, a teenage resident pointed out where an Israeli sniper had been positioned hours earlier.
Fayza Abu-Qutna, 60, said she was tired of Israeli raids on the camp, where she has lived for decades.
"Every time they come to Jenin it is destroyed," she said.
"We live in sadness, we live in misery."
