Images showed the children holding balloons and stuffed animals after touching down at the capital Bishkek's Manas airport early Tuesday.
Scores of women from Central Asia are serving jail time in Iraq over their participation in the activities of jihadist organisations, chiefly the Islamic State group. In many cases, their husbands are assumed to have died in the fighting.
Kyrgyzstan's foreign ministry said in a statement that the repatriation of 79 children born to Kyrgyz parents was "carried out with the consent of their mothers, who remain in the Republic of Iraq."
The statement did not mention the status of the women.
It added that government services will work on the children's "rehabilitation and resocialisation for further transfer to relatives".
Kyrgyzstan is the fourth state in former Soviet Central Asia to complete a repatriation mission from either Iraq or Syria following neighbours Kazakhstan, Uzbekistan and Tajikistan.
The Kyrgyz government thanked Iraq's government, the United Nations children's agency UNICEF and the International Red Cross and Red Crescent Movement.
A fifth Central Asian state, Turkmenistan, has not acknowledged its citizens joining the conflicts in Syria and Iraq.
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