She said some of the women were taken into custody immediately after arriving in Germany.
“The 27 children are, at the end of the day, victims of ISIS, and they have a right to a better future far from its deadly ideology, and also to live in security, as we would wish for our own children,” Ms Baerbock said in a statement.
“The mothers must be held accountable for their actions.”
Germany previously repatriated 23 children and their eight mothers from Al Roj in October. At the same time, neighbouring Denmark brought home 14 children and three women.
Ms Baerbock thanked Kurdish authorities in Syria and “our US partners, who once again provided us with logistical support".
With Wednesday’s operation, “the majority of the German children whose mothers are willing to return to Germany have been brought to safety”, she said.
“There are now only a few special cases for which we are continuing to work on individual solutions.”
Federal prosecutors said on Thursday that four women had been arrested on arrival at Frankfurt Airport — three German citizens, identified in line with local privacy rules only as Nadine K, Gulseren T and Emilie R, and a German-Moroccan dual citizen identified as Fatiha B.
All are accused of membership in a foreign terrorist organisation and Nadine K of other crimes — including keeping a Yazidi woman as a slave who allegedly was regularly sexually assaulted by the suspect’s husband, with her knowledge.
Prosecutors said they had travelled separately to Syria or Iraq in 2014 and joined ISIS.