To accomplish the appropriate treatment strategies of epilepsy action mechanisms underlying epileptic seizures should be lightened. The identification of epileptic seizure-induced alterations on the brain related to their pathologies may provide information for its action mechanism. Therefore, the current study determined molecular consequences of seizures induced by pentylenetetrazol (PTZ), which is a widely used convulsant agent, on rat brain. The rats were administered subconvulsant (25 mg/kg) and convulsant (60 mg/kg) doses of PTZ during a week, and brain tissues were studied by Fourier transform infrared (FT-IR) spectroscopy. Results revealed a decrease in lipid fluidity and lipid and protein content and also the differences in membrane packing by changing the nature of hydrogen bonding as indicated by the C═O, the PO(-)2 symmetric, and asymmetric bands. Monitoring of the olefinic band elicited seizure-induced lipid peroxidation further confirmed by the thiobarbituric acid (TBAR) assay. Additionally, PTZ-induced convulsions led to alterations in protein structures obtained by neural network (NN) predictions like an increase in random coils. On the basis of the spectral changes, treated samples could be successfully differentiated from the controls by cluster analysis. Consequently, the convulsive dose of PTZ caused more significant molecular variations compared to the subconvulsive one. All findings might have an important role in understanding the molecular mechanisms underlying epileptic activities.