Image copyright AFP Image caption More than a third of those new arrivals are minors, according to UNICEF
Nearly 19,000 children have crossed the Darien Gap overland since January, a vast majority fleeing violence in the Democratic Republic of Congo.
Between 300 and 500 people enter the so-called “Silk Route” per day, a UN report says.
Children under the age of 12 make up the bulk of those crossing the desert under the scorching sun.
The Department of Safety and Security of the Economic Community of Central African States (Cecas) says the region has been shaken by growing insecurity.
“The steep terrain, a shortage of roads, the presence of security forces, or even… in some cases foot soldiers is liable to make entry and exit extremely dangerous, if not deadly,” it said.
According to UNICEF, child trafficking, sexual abuse and exploitation remain among the significant threats.
‘People want to go home’
The report’s authors also say more children are being kidnapped, raped and forced into gang recruitment in northern Uganda, eastern Democratic Republic of Congo and western Gabon.
They are mainly seeking an improved quality of life with better schools and healthcare, says the UN High Commissioner for Refugees.
The BBC’s Sylvia Michael said women and children made up a large part of the men crossing from Senegal to the Democratic Republic of Congo, despite fears the boys would be raped and exploited by warlords and armed groups.
It is hoped many will be reunited with their families who had already fled or were fighting the forces who had taken their family members from them.
“Children today want to go home, this is an urgent issue and the situation is complex because the instability in eastern Congo is of course a challenge,” Josette Sheeran, the head of UNICEF in the world’s youngest country, told the BBC.
“We must strengthen the capacity of government, we must strengthen our own capacity, and the international community must increase its capacity as well so we can do a better job.”
The report also noted an alarming increase in people fleeing to the five countries from South Sudan, Ethiopia, Eritrea, Djibouti and Uganda.