The population of Kosovo, which declared independence from Serbia in 2008, is nominally 90 percent Muslim, but largely secular in outlook.
More than 300 Kosovo citizens have travelled to Syria since 2012 and 70 men who fought alongside militant groups were killed.
“Today in the early hours of the morning an important and sensitive operation was organised, in which the government of Kosovo with the help of the US has returned 110 of its citizens from Syria, Kosovan justice minister Abelard Tahiri said at a press conference.
Mr Tahiri did not specify what role the US had played but a plane with a US flag on its tail was seen in the cargo area of Pristina airport as the operation was ongoing.
Authorities said among those who were returned were four fighters, 32 women and 74 children, including nine without a parent.
The four fighters were immediately arrested.
After several hours at the airport, two busloads of women and children were transported under police escort to an army barracks just outside Pristina.
Police said 30 Kosovan fighters, 49 women and eight children still remained in the conflict zones.
“We will not stop before bringing every citizen of the Republic of Kosovo back to their country and anyone that has committed any crime or was part of these terrorist organisations will face the justice,” Mr Tahiri said.
"As Kosovo, we cannot allow that our citizens be a threat to the West and to our allies."
International and local security agencies have previously warned of the risk posed by returning fighters.
In 2015, Kosovo adopted a law making fighting in foreign conflicts punishable by up to 15 years in jail.
There have been no Islamist attacks on its soil, although more than 100 men have been jailed or indicted on charges of fighting in Syria and Iraq. Some of them were found guilty of planning attacks in Kosovo.