A method system and controller for controlling fluid flow in a rotational atherectomy device. A source of fluid is provided through a pump to the rotational atherectomy device, wherein the pump maintains the fluid flow at a minimal rate during a time period when a drive shaft of the device is not rotating. A first control is activated to increase a rate of the fluid flow and second control is activate to initiate a rotation of the drive shaft during another time period when the fluid flow is at the increased rate.