"We are seeing single mothers and children stranded in Greece, Serbia and Bulgaria who have not seen their husbands and fathers for months or even years," said Afshan Khan, UNICEF regional director and special coordinator for the refugee and migrant crisis in Europe.
"The family reunification process is slow, and its outcome uncertain, and it is this uncertainty which can cause significant emotional distress and anxiety for children and families, setting them back for years to come," she added.
According to the agency, most family reunification requests are made in Greece, where 5,000 such appeals were documented in 2016.
UNICEF reported that 700 of these were made by unaccompanied and separated children, and that only 1,107 applicants eventually made it to their destination countries by the end of the year.
Along with Greece, Hungary and Bulgaria, other countries in the western Balkans have also played host to an increasing number of stranded refugee and migrants.
Figures show that nearly 80,000 refugees and migrants were stuck in these states by the end of April this year, up from 47,000 in March 2016.
"Keeping families together is the best way to ensure that children are protected, which is why the family reunification process for refugee and migrant children is so important," Khan said.