The Spanish women were arrested upon landing in Madrid and will be brought before a judge at the Audiencia Nacional, Spain's highest criminal court, on terror charges.
The children were taken into the care by social services in the Madrid region.
“The government has just repatriated two women and 13 Spanish minors from Syrian refugee camps,” a Foreign Ministry statement said.
They arrived at Torrejon de Ardoz military airport nearly two months after the Spanish government had agreed to bring them home.
The women will appear in court on Wednesday on “terrorism-related charges”, a court spokesman said.
The ministry said the extradition had taken “several months” because of the “complexity [of the operation] and due to the high-risk situation in the Syrian camps”.
El Mundo daily newspaper said the pair arrived with their nine children, aged between three and 15. El Pais daily reported that the other four were orphans who were being looked after by one of the women.
One of the women is reportedly married to a jailed ISIS fighter and the other is widowed.
They will face charges of co-operating with a terror organisation and could be sentenced to five years behind bars.
The women had been held in various detention camps in Syria since 2019.
Spain has also agreed to repatriate a Moroccan woman — along with her three children — who was married to a Spanish fighter who died, but the family fled a detention camp near Iraq in 2020 and their whereabouts remains unknown.