The inscription over the main entrance dates Kali Mosque to 1370 AD. This mosque has a similar layout as that of Khirkee Mosque. Its name is probably due to the black (kali) patina that once encrusted the rendering. This mosque was in ruins at the beginning of 20th Century and restoration has eliminated many contemporary features.
This mosque was built by Prime Minister of Firoz Shah Tughlaq – Khan Jahaan Junan Shah. He built seven Mosques in Delhi – Kalan Masjid, Khirki Masjid, Begumpur Mosque, Kalu Sarai Masjid, Kali Masjid in Nizamuddin Area, A Mosque near wall of Shahjahanabad and Chausath Khamba.