A diagnostic and heat management system for a fuel cell stack is provided herein that includes a diagnostic control analyzer that diagnoses and analyzes a state of the fuel cell stack by measuring a voltage and a current of the fuel cell stack. Also, an AC signal generator generates a diagnostic AC signal, and an AC component driving element that is included in an AC component in a current of the fuel cell stack. Additionally, a termoelement is driven as a heat absorbing device when a temperature of the AC component driving element is equal to or greater than a predetermined temperature and is driven as a heat emitting device when a temperature of the AC component driving element is less than a predetermined temperature, in order to manage heat generation in the AC component driving element.