The thermopower properties of GaN nanowires with transitional metal impurities are investigated in the framework of constrained spin density functional theory (DFT) calculations. The nanowires are connected to nanoscopic Al electrodes, which ensure a natural coupling to the wurtzite structure of the nanowires. We investigate the thermoelectric properties comparatively for the pristine GaN nanowire and the system with one Mn adatom. Our study points out the predicted qualitative behavior for systems with a peak in the total transmission, as well as the sign change in the thermopower. For the system with the magnetic impurity we find an enhanced conductance, thermopower and figure of merit. The detectable spin current polarization suggests the device structure may be also used in low temperature sensing applications.