Among other new device concepts, nickel silicide (NiSix)-based Schottky barrier nanowire transistors are projected to supplement down-scaling of the complementary metal-oxide semiconductor (CMOS) technology as its physical limits are reached. Control over the NiSix phase and its intrusions into the nanowire is essential for superior performance and down-scaling of these devices. Several works have shown control over the phase, but control over the intrusion lengths has remained a challenge. To overcome this, we report a novel millisecond-range flash lamp annealing (FLA)-based silicidation process. Nanowires are fabricated on silicon-on-insulator substrates using a top-down approach. Subsequently, Ni silicidation experiments are carried out using FLA. It is demonstrated that this silicidation process gives unprecedented control over the silicide intrusions. Scanning electron microscopy and high-resolution transmission electron microscopy are performed for structural characterization of the silicide. FLA temperatures are estimated with the help of simulations.