Introduction. Stress during puberty exerts long-term effects on endocrine systems and brain structures, such as the prefrontal cortex (PFC) and basolateral amygdala (BLA), two cerebral areas that participate in modulating sexual behavior and whose functioning is regulated by androgenic hormones. Objective. To evaluate the effect of pubertal stress due to social isolation on the sexual motivation, serum testosterone levels, and electroencephalographic activity (EEG) of the PFC and BLA in male rats. Method. Sixty sexually-experienced male rats were used. Thirty were stressed by social isolation during puberty (SG, housed 1 per cage, postnatal days 25-50); the other 30 formed the control group (CG, 5 per cage). All rats were implanted bilaterally with stainless steel electrodes in the PFC and BLA. EEGs were recorded during the awake-quiet state in two conditions: without sexual motivation (WSM), and with sexual motivation (SM). After EEG recording, the rats were sacrificed by decapitation to measure their testosterone levels. Results. SG showed lower sexual motivation and testosterone levels, but higher amygdaline EEG activation in the presence of a receptive female, while CG showed higher prefrontal EEG activation. Discussion and conclusion. It is probable that the decreased testosterone levels resulting from pubertal stress affected prefrontal and amygdaline functionality and, hence, sexual motivation. These data could explain some of the hormonal and cerebral changes associated with stress-induced sexual alterations, though this suggestion requires additional clinical and animal research.