At least 3,700 children in Guinea, Liberia and Sierra Leone who have lost one or both parents to Ebola this year face being shunned, the UN children's organisation has said.
Carers were urgently needed for these orphans, Unicef said.
A basic human reaction like comforting a sick child has been turned "into a potential death sentence", it added.
The World Health Organization (WHO) says more than 3,000 people have died of Ebola in West Africa.
It is the world's most deadly outbreak of the virus.
The figure on the number of Ebola orphans follows a two-week assessment mission by Unicef to the three countries worst-affected by the outbreak. An earlier version of this story said that 4,900 children had lost parents but the correct figure is 3,700.
It found that children as young as three or four years old were being orphaned by the disease.
Children were discovered alone in the hospitals where their parents had died, or back in their communities where, if they were lucky, they were being fed by neighbours - but all other contact with them was being avoided.
"Thousands of children are living through the deaths of their mother, father or family members from Ebola," Unicef's Manuel Fontaine said in a statement.
"These children urgently need special attention and support; yet many of them feel unwanted and even abandoned.
"Orphans are usually taken in by a member of the extended family, but in some communities, the fear surrounding Ebola is becoming stronger than family ties."
Liberia's chief medical doctor Bernice Dahn tells the BBC about the challenges of her self-imposed 21-day quarantine, after one of her assistants died from the deadly Ebola virus:
"It is the right thing to do and to send a strong message to the Liberian people. If we were just disciplined enough and everybody was obeying rules, we wouldn't be here today.
I'm sleeping in a room all by myself - my husband has moved into the guest room. At home I use my own utensils, I disinfect them myself so others don't get infected.
Physically I am fine, mentally like any other human being [there is] the fear of the unknown.
My husband… my children have been supportive. The difficulty is the way we used to sit down in the evening, everyone watched TV together laughing and joking. These days they are in their rooms to watch their own TV and I'm in my room to watch mine.
I have my grandson here who I can't hold. He will walk to me and I will tell him: 'Go back to your mummy.'"
The number of Ebola orphans has spiked in the past few weeks and preliminary reports suggest that it is likely to double by mid-October, Unicef said.
There was an urgent need to establish a system for identifying and caring for Ebola orphans, it added.
Unicef will be holding a meeting on the issue in Sierra Leone next month but before then it wants potential carers to come forward.
"Ebola is turning a basic human reaction like comforting a sick child into a potential death sentence," Mr Fontaine said.
"We cannot respond to a crisis of this nature and this scale in the usual ways. We need more courage, more creativity, and far far more resources."
Meanwhile, the head of the new UN mission to combat Ebola says there needs to be significant progress in fighting the disease within the next 60 days.
Anthony Banbury said 70% of infected people should be receiving treatment and 70% of burials should be done safely within that period.
"It's an extremely ambitious target and the only way it will be achieved is through this international effort," he told reporters.
The UN Secretary General Ban Ki-moon set up the UN Mission on Ebola Emergency Response earlier this month.
Ebola virus disease (EVD)
- Symptoms include high fever, bleeding and central nervous system damage
- Spread by body fluids, such as blood and saliva
- Fatality rate can reach 90% - but current outbreak has mortality rate of about 70%
- Incubation period is two to 21 days
- There is no proven vaccine or cure
- Supportive care such as rehydrating patients who have diarrhoea and vomiting can help recovery
- Fruit bats, a delicacy for some West Africans, are considered to be virus's natural host