Mahabad is situated in a region that was the center of the Mannaeans, who flourished in 10th to 7th centuries BC. Mannaeans "after suffering several defeats at the hands of both Scythians and Assyrians, the remnants of the Mannaean populace were absorbed by an Iranian people known as the Matieni and the area became known as Matiene. It was then annexed by the Medes in about 609 BC.

In the medieval period, the Kurdish dynasty of Hasanwâyhids (959-1015) was ruling the region. After destruction under the Mongols, Ilkhanate, and Timurid dynasty, the region was controlled by Kara Koyunlu (1375–1468) and Aq Qoyunlu (1378–1501)(both Oghuz Turkic tribes). As Muhamed Amin Zaki in his book, A Short History of the Kurds and Kurdistan, during regional conflicts between Kara Koyunlu and Aq Qoyunlu, the Mukri Kurds gained power in the fertile valleys of south of Lake Urmia.

Murki Kurds participated in several wars between Safavid dynasty and Ottoman Empire, and gained more predominance. In 17th century AD, Mahabad became the seat of Mukri principality (known as Murkriyān in Kurdish and Morkriyān in Persian). Many believe Budaq Sultan Murki, who built Mahabad's Jameh Mosque is the founder of the current city.