The mosque was built in 1580, according to two inscriptions on the mosque. The mosques mihrab tiles are from the İznik tile workshop, which was known for its high-quality products. The mosques calligraphy is by Demircikulu Yusuf Efendi, who is considered the last representative of the Karahisari school of calligraphy. The mosque is part of a complex that also includes a tomb, madrasa, and hammam. The mosque is said to have been built on the sea because Kılıç Ali Pasha was ordered to do so by Sultan III. Murad. The sultan told Kılıç Ali Pasha to build a mosque on the sea because he was the Grand Admiral. Kılıç Ali Pasha agreed and built the mosque on a foundation of stone, earth, and rubble on the edge of the Tophane pier. This is why Kılıç Ali Paşa Mosque is said to be the first mosque built on the sea.