Previous studies have observed increases in electroencephalographic power during sleep in the spindle frequency range (approximately 11–15 Hz) after exposure to mobile phone-like radio frequency electromagnetic fields (RF EMF). Results also suggest that pulse modulation of the signal is crucial to induce these effects. Nevertheless, it remains unclear which specific elements of the field are responsible for the observed changes. We investigated whether pulse-modulation frequency components in the range of sleep spindles may be involved in mediating these effects. Thirty young healthy men were exposed, at weekly intervals, to three 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, and a sham control condition. Both active conditions had a peak spatial specific absorption rate of 2 W kg−1. During exposure subjects performed three different cognitive tasks (measuring attention, reaction speed and working memory), which were presented in a fixed order. Electroencephalographic 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, our 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.