Solution verification is performed to quantify the numerical uncertainty of Nusselt numbers in micro-scale heat sinks obtained from 3-D numerical simulations. A numerical procedure is first developed to calculate local and average Nusselt numbers along 4 different miniature heat sinks. Validation process is performed by comparing the obtained numerical results experimental data. Fairly good agreement between numerical results and experimental data confirms the reliability and accuracy of the proposed numerical procedure. The observed order of accuracy for water flow in a micro-tube with constant uniform heat flux is 1.81 while the observed order of accuracy for conjugate heat transfer of water flow within a microchannel heat sink is estimated as 1.2. The numerical uncertainty for local Nusselt numbers within the investigated microchannel heat sink is estimated to be 0.13.