In a system and method for conditioning air in a vehicle, it is determined whether an inside air temperature detected by an inside air temperature sensor is stable, an outside air temperature is estimated based on the inside air temperature only when the inside air temperature is stable, a target conditioned air temperature is calculated using an estimated outside air temperature as well as the estimation of outside air temperature is repeated, and the estimated outside air temperature used for the calculation of the target conditioned air temperature is renewed only when the estimated outside air temperature is different from a prior estimated outside air temperature by a value more than a predetermined value. The outside air temperature is adequately estimated without providing an outside air temperature sensor. Consequently, a desirable air conditioning for vehicles may be performed simply and inexpensively.