MPPT solar charge controllers are used when the voltage of the solar panels is significantly greater than the required charging voltage.  Typical solar panels work at 15-17V, whereas typical charging voltages for a 12V system may be 10-15V. This surplus energy is effectively wasted as PWM controllers cannot boost voltage to maintain charge current. 

MPPT controllers overcome this problem by being able to optimise the charge voltage and current. MPPT charge controllers typically store charge within them and boost the current of the charge output as and when needed. By doing this, they are able to increase the amount of charge current by 10-15%.