Anwar Ali Abidi and another person sustained injuries when the motorcycle-borne assailants opened fire at the doctor's clinic in the city's Nazimabad area, said a senior police official.
Abidi later succumbed to his injuries.
Police suspect the incident was the result of a target killing.
Karachi, the largest metropolitan city of Pakistan, is riddled with targeted killings, gang wars, kidnappings for ransom, extortion and terrorism.
On April 19, prominent rights activist Sabeen Mahmud was gunned down in the city.