Aspartame is a non-nutritive sweetener that is used predominantly in various 'diet' and 'low-calorie' products, such as beverages, instant breakfasts, desserts, breath mints, sugar-free chewing gum, vitamins, and pharmaceuticals, consumed by millions of people who are attempting weight loss, young adults and diabetic persons. On a weight basis, the metabolism of aspartame generates approximately 50% phenylalanine, 40% aspartic acid and 10% methanol. The detailed mechanisms of the effects of aspartame on the electrophysiological response are still unclear; therefore, this study was designed to clarify whether longer-term aspartame consumption has any effect on the electrophysiological response in Wistar albino rats. The oral administration of aspartame in a safe dose of 40 mg/kg bodyweight/day (as recommended by EFSA, 2012) was tested in Wistar albino rats for a longer period (90 days). Electrophysiological responses, including heart rate variability (HRV) and electroencephalogram (EEG) pattern, were assessed in a folate-deficient animal model along with control animals using BIOPAC and EEG equipment (model RMS EEG-24 brain new-plus: RMS-Recorder and Medicare systems). In this study, the folate-deficient animal model was used to mimic human methanol metabolism in rats. After 90 days of aspartame treatment, a significant alteration was observable in the time domain [Mean RR (ms) SDNN (ms) RMSSD (ms) PNN50 (%)] and the frequency domain [LF, HF, and LF/HF ratio] with significantly impaired frequency and amplitude of the fronto-parietal and occipital EEG waves at p ≤ 0.05. The results of this study clearly indicate that the oral consumption of aspartame reduced HRV, with sympathetic dominance and loss of vagal tone, and altered sympathovagal activity along with impairment of learning and memory, showing an additional effect on health within this study duration. The aspartame metabolites methanol and formaldehyde may be the causative factors behind the change observed.