Yes. There are four wires going to a PWM fan:
Ground
+12 Volts
Tach signal from the fan to tell the computer how fast the fan is turning
+5 volt PWM signal
The PWM signal is pulsed on and off. Very long pulses to spin the fan faster. Short pulses to slow the fan down.
There is a little circuit board inside your PWM fan that reads the pulses from the control signal and varies the +12 volt input to adjust the speed of the fan proportional to the control signal.
The BIOS/motherboard circuitry generates the PWM control signal based on temperature readings (for example, the CPU temperature).
You can also plug a three-pin fan into the 4-pin connectors. There simply won't be a PWM control signal and the fan will run wide open at the full...