Perhaps you are asking how a 50% duty cycle results in 2.5volts when the actual voltage is either 5volts or 0volts?
The answer is that whatever is using the current averages it. For example the average current through a resistor will be half what it would be if the voltage was constant at 5 volts. If the current is used to light an LED it will be on for half the time and off for half the time and your eye will average the light and see a dim LED.