Previous studies have observed increases in EEG power during sleep in the spindle frequency range (approx. 11–15 Hz) after RF EMF exposure synthesizing GSM conditions. This study investigated whether pulse-modulation frequency components in the range of sleep spindles may be involved in mediating these effects. 30 young healthy men were exposed, at weekly intervals, to 3 different conditions for 30 min directly prior to an 8-h sleep period. Exposure consisted of a 900-MHz RF EMF, pulse modulated at 14 Hz or 217 Hz (psSAR of 2 W/kg), and a sham control condition. During exposure, subjects performed three different cognitive tasks (measuring attention, reaction speed and working memory), which were presented in a fixed order. EEG power in the spindle frequency range was increased during non-rapid eye movement sleep (2nd episode) following the 14-Hz pulse-modulated condition. A similar but non-significant increase was also observed following the 217-Hz pulse-modulated condition. Importantly, this exposure-induced effect showed considerable individual variability. Regarding cognitive performance, no clear exposure-related effects were seen. Consistent with previous findings, the results provide further evidence that pulse-modulated RF EMF alter brain physiology, although the time-course of the effect remains variable across studies. Additionally, we demonstrated that modulation frequency components within a physiological range may be sufficient to induce these effects.