A fan coil controller for a hot and cold water system of a building that turns off the fan while the hot water and cold water coils are flushed. A fan coil control circuit is configured to periodically and temporarily operate a hot water flow control circuit and a cold water flow control circuit to cause a flushing of the hot and cold water system and simultaneously provide a signal to a fan control circuit to prevent the thermostat enabling the fan during flushing of the hot and cold water system.