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This paper reports the synthesis of novel nanocomposite based on multi-walled carbon nanotubes (MWCNT) covalently bonded by molecularly imprinted poly(methacrylic acid-hemin) (MIP-MWCNT) using tert-butylhydroquinone (TBHQ) as template molecule and its use in the construction of electrochemical sensor. Chemical, physical and morphological structure of nanocomposite was characterized by FT-IR, TGA, SEM, TEM and textural analysis. The electrochemical sensor highly selective to TBHQ was prepared by drop-casting a suspension of nanocomposite on the surface of a glassy carbon electrode. From cyclic voltammetry, it was observed that the electrochemical sensor modified with MIP-MWCNT exhibited great recognition performance, higher analytical response and catalytic properties towards the TBHQ when compared to NIP-MWCNT (nanocomposite polymerized without adding TBHQ), MIP-MWCNT without hemin and MIP-hemin without MWCNT. Such results demonstrated the synergic effect of imprinting influence, MWCNT and hemin in improving the performance of electrochemical sensor. From chronoamperometric measures, the electrochemical sensor modified with MIP-MWCNT could recognize TBHQ selectively in the presence of electroactives and structurally similar compounds. Under optimized conditions by pulse differential voltammetry (pulse amplitude of 100 mV, pulse time of 25 ms and scan rate of 10 mV s−1) and measures in 0.15 mol L−1 H2SO4, the proposed method successfully enabled the simultaneous determination of TBHQ and butylated hydroxyanisole (BHA), yielding limits of detection of 0.85 and 0.50 μmol L−1, respectively. The feasibility of the method was checked by simultaneous determination of TBHQ and BHA in soybean oil, margarine, mayonnaise and biodiesel, whose results were statistically equal to those achieved by high performance liquid chromatography (HPLC).