We report here the effect of thermal annealing on the thermal conductivity of ZnTe nanowires measured on a microfabricated suspended device. Molecular dynamics simulation was used to calculate the effect of contacts on the measurements at different temperatures and to estimate the intrinsic nanowire thermal conductivity values. A decrease in thermal conductivity was observed after each thermal annealing step at all the measured temperatures. Thermal annealing can be a potential method to improve the thermoelectric efficiency of nanowires, not only by enhancing the electrical conduction as demonstrated before, but also by suppressing the thermal transport at the same time.