The Ministry of Women, Children and Social Welfare said the ban is aimed at protecting homeless children who are living in tent camps where there are large numbers of people.
Ministry official Ram Prasad Bhattarai said an approval letter issued by a district Child Welfare Board will be needed for any other adults traveling with children from one district to another.
The ban comes days after police stopped two groups of children who were being taken by unrelated adults by bus in different districts. The children are being held in government shelters and police are still investigating the cases.
Thousands of children are taken from Nepal to neighboring India every year to work as child laborers or in brothels.
The earthquakes on April 25 and May 12 killed at least 8,673 people in Nepal.