In hard-hit Pakistani-administered Kashmir, about 800,000 children were being immunised for diseases including measles, polio, diphtheria and tetanus, said Dr Edward Hoekstra, a senior health adviser for Unicef.
A similar campaign is already under way in Pakistan's North West Frontier Province, which was also devastated by the quake.
Shots will include vitamin A to guard against respiratory illnesses expected as harsh winter weather descends on the Himalayan region, Hoekstra said.
In all, Unicef and the Pakistani Health Ministry plan to immunise 1.2 million children.
"Now, the mourning period is over and everybody is ready to move forward to make sure that those who carry the future will be protected," Hoekstra said in the Pakistan Kashmir hub of Muzaffarabad.
"We are starting in the most inaccessible areas in case the weather turns bad in the next two weeks," he said.
In a third exchange of aid since the 8 October quake, porters from Pakistan and India carried sacks of rice and blankets across a bridge over the Neelum river at the Nauseri-Teethwal crossing.
Area residents voiced frustration at delays in implementing a much-heralded agreement to allow Kashmiris from either side of the divided region to cross over to visit relatives and friends.
Indian and Pakistani soldiers
meet across the Line of Control
"I wish I could have crossed over to see my relatives. This does not make sense," said Teethwal resident Abdul Qadeer, sitting on the Indian side of the river.
The two sides agreed on 30 October to open five crossing points.
Plans for reunions have been delayed in part because both countries need to scrutinise lists of travellers, and India fears separatist Muslims fighting New Delhi's rule in Indian-administered Kashmir may be among them.
The 7.6-magnitude quake killed about 86,000 people in Pakistan's portion of the territory and another 1350 in India.
It destroyed bridges, roads, and the homes across a wide swath.
Quake relief, compensation for lost livelihoods and reconstruction costs will total about $5.2 billion, the Asian Development Bank and World Bank said in a report that will be used at a two-day donors' conference opening on Friday in the Pakistani capital.
The quake destroyed the homes of more than three million people and aid agencies have been busy distributing tents for survivors descending from remote, high-elevation settlements to seek shelter in regional hubs.