An HVAC system includes a variable speed electric motor driven fan for circulating air to an enclosed space through an indoor unit for providing heating or cooling effect to air circulated through the indoor unit. A controller with user or system installer actuatable switches includes a programmable microcontroller providing a pulse width modulated (PWM) signal to a motor control unit to select a predetermined air flowrate less than full air flowrate during system startup and shutdown. User input parameters include selected percentages of full air flowrate to satisfy requirements for reduced noise level, lower humidity and for improved sensible heating of air being circulated, the latter being effective particularly for heat pump applications. Selection of pre-run, short run and shutdown cycles may be provided.