Israel also continued its precautionary culling of hundreds of thousands of birds on Sunday, and Jordan, which is free of the deadly H5N1 strain of the virus, responded to the developments by stepping up measures to combat the disease.
Nasser el-Sayyed, the deputy health minister, said the man was recovering in the hospital after being admitted on Thursday with a fever.
Police said the man came from the village of Noqbas. Residents there were uneasy after the announcement.
Um Mohammed, 35, said that although she had told authorities that her birds were dying, "They did nothing to help me. Day after day, I watched my chickens die. I felt as though I was handcuffed."
The country's first known human case, a woman who died on Friday, was also from Qalyoubiya.
The two victims had not had any contact and were from different villages, the Health Ministry said.
The Egypt-based US Naval Medical Research was conducting additional tests to confirm whether the latest case was H5N1.
Turkey and Iraq are the only other Middle Eastern countries where humans have died of the virus.
Israeli veterinary officials have continued to slaughter of hundreds of thousands of birds as new tests came close to confirming Israel's first outbreak of the deadly bird flu.
The alert had been raised on Wednesday when thousands of turkeys started dying.
Dafna Varisca, an Agriculture Ministry spokeswoman, said, "It's very close to 100%" sure that the virus has spread to Israel.
Saeed Darwazeh, the Jordanian health minister, said the country was still free of the H5N1 strain.
Nonetheless, it was stepping up monitoring efforts by visiting farms and looking for any increase in poultry deaths, said Adel al-Balbissi, director of the unit tackling bird flu at Jordan's Centre for Disease Control.
"We have increased our preparedness to the maximum as fears have increased of a bird flu outbreak … because it could happen anytime," al-Balbissi said.
The H5N1 strain of bird flu has killed nearly 100 people worldwide, according to the World Health Organisation, and caused millions of birds to be killed.