For the first time, electrocatalytic oxidation and selective determination of methadone (Mtd), as a long acting opioid, in the presence of acetaminophen (Ac) has been investigated at a glassy carbon electrode modified with functionalized multi-walled carbon nanotubes. This simple and sensitive electrochemical sensor was fabricated through the drop-casting of functionalized multi-walled carbon nanotubes (fMWCNT) on the surface of a glassy carbon electrode (GCE). The electrocatalytic oxidations of Ac and Mtd are both individually and simultaneously investigated at the surface of the fMWCNT modified glassy carbon electrode (fMWCNT/MGCE) through using cyclic and differential pulse voltammetric studies. The fMWCNT/MGCE offered a considerable enhancement in the anodic peak current of Ac and Mtd associated with separating their overlapping voltammetric responses with potential difference of 290 mV. The catalytic peak currents obtained from differential pulse voltammetry of Ac and Mtd increased linearly with their concentration at the ranges of 0.45–90.0 M and 0.5–100.0 M, respectively, and the detection limits for Ac and Mtd were sequentially 0.35 M and 0.28 M. Furthermore, this electrochemical sensor was successfully implemented for the quantitative determination of Ac and Mtd in human urine, saliva and pharmaceutical samples using standard addition method and the obtained results were found to be satisfactory.