The Turkish International Cooperation and Coordination Agency funded the restoration project.
Erdogan attended the ceremony of the restored mosque via a video link from Ankara.
In his address, the Turkish president said Kosovo is a friendly country and, therefore, Turkey will continue to allocate it resources through various TIKA projects.
"From the capital of Turkey, Ankara, we welcome everyone, ministers in the Kosovo government, representatives of the Islamic community, students, teachers and our Kosovar brothers. Congratulations to the re-opening of this beautiful Emin Pasha mosque and we wish you good luck," he said.
TIKA's Kosovo coordinator Eyup Umutlu said the Turkish organization is preserving the country’s cultural and historical heritage.
"The restoration of mosques like this one has a special meaning…[it] shows that Muslims here have existed for centuries," Umutlu said.
The Emin Pasha Mosque was built in 1832 and is considered as one of the most beautiful mosques in Kosovo.
Turkish envoy in Prizren, Selen Evcit, Islamic Community of Kosovo President Naim Ternava, Minister of Environment and Spatial Planning, Ferid Agani, Turkish members of Kosovo Assembly as well as representatives of TIKA and the Institute "Yunus Emre" in Kosovo attended the ceremony.