Magnetic nanoscale compounds and alloys of gadolinium are promising materials for technological and medical applications. In this paper the influence of structural defects on the properties of the binary GdSi nanopowders formed in laser ablation and post-irradiation processes have been investigated. To obtain compound GdSi nanoparticles (NPs) we used laser ablation of a combined target consisting of Gd and Si plates tightly pressed to each other with focusing a laser beam onto the gadolinium–silicon interface. The crystalline structure, phase composition of the NPs formed were examined by SEM and X-ray diffraction (XRD). Magnetic measurements showed that the resulting NPs did not exhibit hysteresis at low temperature (6 K), which is typical to nanosized magnetic materials demonstrating superparamagnetic behavior. Magnetization increased after laser processing of the samples due to ordering in the grain structure and in the magnetic moments at the surface.