A velocity sensor, a controller, a plunger lift system and method for controlling a plunger lift system is provided. The velocity sensor can use a first magnetic field sensor and a second magnetic field sensor spaced a sensor distance to determine a velocity of a plunger as it passes the velocity sensor. The controller can use information received from the velocity sensor to both control the operation of the plunger lift system using the measured plunger velocity obtained from the velocity sensor and shut down the well if the plunger is measured travelling too fast.