Sofi Sinan Pasha[1] started construction of the mosque in either 1600 or 1608.[2] Sofi Sinan Pasha, an Albanian and former beylerbey and kaymakam in Bosnia should not be confused with grand vizier Sinan Pasha, who built the Sinan Pasha Mosque in the nearby city of Kaçanik.[1]

It is widely considered that the stones used to build the mosque were taken from nearby Holy Archangels Monastery, a Serbian Orthodox monastery founded by Serbian Emperor Stefan Dušan.[1][3] In fact, parts of the former monastery can be seen in the mosque.[2] The monastery, which was abandoned after the arrival of the Ottomans in the 16th century, had fallen to ruins by the 17th century. Hasan Kaleshi, an Albanian historian, sustained in 1972 that Sofi Sinan Pasha couldn't have possibly ordered any monastery destruction as this was impossible without a Sultan decree, rather, he ordered the use of the spare stones to a better deed as ordered by the Sultan.[1]

Sinan Pasha Mosque was declared a Monument of Culture of Exceptional Importance in 1990 by the Republic of Serbia.[4]