If your HVAC unit isn't operating as well as it once did, it's time to replace it. The cost of replacing a whole HVAC unit ranges from $5,000 to $10,000, with the national average being $7,000. This equates to between $25 to $60 per square foot. Prices are determined by the size and brand of the HVAC system, the size of the house, the length of the ductwork and the efficiency rating of the new unit.