The medial prefrontal cortex (mPFC) and basolateral amygdala (BLA) participate in the modulation of several motivated behaviors, such as the sexual behavior. Both structures are sensitive to stress when it is experienced mainly in critical periods of the life-cycle, such as the prenatal period. This study evaluated the effects of prenatal stress on electroencephalographic activity (EEG) of the mPFC and BLA during sexual motivation. EEG was recorded in the mPFC and BLA of male rats assigned to either a prenatally-stressed group (SG, dam immobilized from days 14 to 21of pregnancy), or a control group (CG), during the following conditions: awake-quiet state without sexual motivation, and awake-quiet state with sexual motivation. Compared to CG, fewer SG subjects presented copulatory responses and their levels of sexual motivation were lower. The CG subjects with sexual motivation showed a higher absolute power (AP) of the 14–30 Hz band in the left mPFC and BLA than those without sexual motivation. The SG showed a lower AP of the 4–7 and 8–13 Hz bands in the left BLA. Thus, prenatal stress suppressed the prefrontal and amygdaline EEG changes associated with a sexually-motivated state. EEG data show that stress affects the functioning of these two brain structures and so could interfere with the adequate processing of sexual stimuli. These findings contribute to understanding the brain mechanisms that underlie the effect of prenatal stress on the processing of sexual stimuli in male rats.