A time of day zoning control system for a heating, ventilating, and air conditioning system is provided. The system utilizes a programmable thermostat and a number of temperature sensors to control the HVAC system to regulate the temperature in a particular location within a dwelling or structure based on consumer preferences. The regulation control will utilize a temperature sensed by a particular temperature sensor at different times throughout the day to control the temperature in that zone to ensure occupant comfort. A single temperature sensor may be selected to control the HVAC system during these different periods, or multiple sensors may be utilized during the same period. When multiple sensors are used, a weighting factor may be used.