To develop an electrochemical sensor for electroactive molecules, the choice and prediction of redox reactive sites of the modifier play a critical role in establishing the sensing mediating mechanism. Therefore, to understand the mediating mechanism of the modifier, we used advanced density functional theory (DFT)-based quantum chemical modeling. A carbon paste electrode (CPE) was modified with electropolymerization of brilliant blue, later employed for the detection of paracetamol (PA) and folic acid (FA). PA is an analgesic, anti-inflammatory and antipyretic prescription commonly used in medical fields, and overdose or prolonged use may harm the liver and kidney. The deficiency of FA associated with neural tube defects (NTDs) and therefore the quantification of FA are very essential to prevent the problems associated with congenital deformities of the spinal column, skull and brain of the fetus in pregnant women. Hence, an electrochemical sensor based on a polymerized brilliant blue-modified carbon paste working electrode (BRB/CPE) was fabricated for the quantification of PA and FA in physiological pH. The real analytical applicability of the proposed sensor was judged by employing it in analysis of a pharmaceutical sample, and good recovery results were obtained. The potential excipients do not have a significant contribution to the electro-oxidation of PA at BRB/CPE, which makes it a promising electrochemical sensing platform. The real analytical applicability of the proposed method is valid for pharmaceutical analysis in the presence of possible excipients. The prediction of redox reactive sites of the modifier by advanced quantum chemical modeling-based DFT may lay a new foundation for researchers to establish the modifier-analyte interaction mechanisms.