We conducted observations of wind velocity profiles above a high-density area in Tokyo, Japan, using a Doppler LIDAR system. Obtained data of the exponent index for the power law, which is commonly used to describe the wind velocity profile, displayed diurnal variation, decreasing in the daytime, which is expected in unstable atmospheric conditions. This paper provides information on the uncertainty in the calculated ventilation airflow rate due to the use of a constant value for the exponent index. The study was performed with data on wind pressure coefficients obtained from a numerical parametric study using computational fluid dynamics based on observation data. The uncertainty was assessed based on comparison of the ventilation airflow rate calculated using a constant value for the exponent index, and the ventilation airflow rate calculated considering a diurnal change in the exponent index. The results indicate that the ventilation airflow rate obtained from a constant value for the exponent index for an isolated building with two openings is underestimated by up to 8% in the daytime. A large relative uncertainty occurs at a lower height, i.e., a large relative error of the approaching wind velocity and a resulting error in the wind pressure coefficient.