The president said in a statement he visited Embla Ademi and her family "to give my support and to raise awareness that inclusion is a basic principle".
The President of North Macedonia walked a girl with Down's syndrome to school this week after hearing she was being bullied.
Stevo Pendarovski visited Embla Adema and her family on Monday in Gostivar, about 65 kilometres south-west of the capital Skopje.
Together they talked about the challenges 11-year-old Embla and her family face every day. He then walked Embla to school.
"The president stressed that the behaviour of those who in any way endanger the rights of children is unacceptable, especially when it comes to children with atypical development," a statement from the president's office said.
"They should not only enjoy the rights they deserve, but also feel equal and welcome at the school desks and schoolyards. It is our obligation, as a state, but also as individuals, and the key element in this common mission is empathy," it added.
"We are all equal in this society," Pendarovski said. "I came to give my support and to raise awareness that inclusion is a basic principle."
The statement added that the president welcomed the decision by the country's ombudsman and Commission for Protection against Discrimination to open a probe into Embla's case.