The error in measuring temperature profiles by thermocouple inside boundary layer mostly comes from the conduction heat transfer of the thermocouple. The error is not negligible when the conductivity of the thermocouple is very high. In this study, the effect of conduction heat transfer of the thermocouple on the temperature profile inside boundary layer was examined by considering both free-stream velocity and a thermocouple position. The conduction error of an E-type thermocouple was investigated by numerical analysis of three-dimensional conjugate heat transfer for various velocity profiles of boundary layer and thermocouple positions.