Highly uniform iron nanowires were synthesized in porous anodic alumina, through a pulsed electrodeposition method. The effect of the rest pulse duration in the deposition quality was systematically investigated, being the best duration found at 0.6 s with 91.9% of pores filled. A methodology of surface response design of experiment was conducted to find the optimum predicted value for the rest pulse duration, by controlling the following experimental parameters/variables: current density, electrolyte concentration and temperature. The influence of the rest pulse in the grain size of the iron nanowires was also studied trough X-ray diffraction patterns. A numerical simulation of the concentration evolution along a nanopore was performed, allowing to achieve a deeper understanding of the importance of the rest pulse in the NW electrodeposition.