Mr Hernandez said that poverty and drug-related violence have led to a sharp increase in the number of children trying to enter the US illegally.
The region lacks the resources to deal with the problem, he said.
Some 57,000 unaccompanied children have arrived at the US border with Mexico since October 2013.
"We have to recognise that our countries can't do it by themselves. We need the support of the US and Mexico in a common problem," Mr Hernandez said.
He was speaking at a special conference in the Honduran capital, Tegucigalpa, to address the problem.
Mr Hernandez said there was a clear link between the violence generated by the drug-trafficking cartels operating in his country and the exodus of children.
"Seven out of nine children who venture on the dangerous journey towards the United States come from the most violent areas of Honduras.
"Those are also the regions where the drug cartels are most active," he said.
Mr Hernandez said the United States should set up in Central American anti-narcotics strategies implemented in Colombia and Mexico.
In both countries, however, critics said that the "war on drugs" policies backed by the United States led to an increase in violence.
The Organization of American States (OAS) President Jose Miguel Insulza called for immediate action.
"There must be an urgent solution to a regional crisis involving several countries," Mr Insulza said at the conference.
Last month, US President Barack Obama announced he was shifting border patrol staff to the US border with Mexico in the face of the "humanitarian crisis".
He also boosted aid to Guatemala, El Salvador, and Honduras, which will all receive millions of dollars to combat gang violence.

Milford Haven Coastguard were alerted to the incident near Blaenplwyf just before 14:40 BST.
A Sea King rescue helicopter from RAF Valley flew the man to Morriston Hospital in Swansea. He has been described as dazed but conscious.
A second man was also rescued from the cliff face but was reported to be uninjured.
RNLI rescue teams from Aberystwyth attended.
Honduras President Juan Hernandez has called on the United States to create an anti-drugs plan for Central America.
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A 24-year-old man has been flown to hospital after falling 30ft (9m) down a cliff onto rocks near Aberystwyth.