An essential biomarker for the early detection of cardiovascular diseases is serum homocysteine (Hcy). In this study, a molecularly imprinted polymer (MIP) and nanocomposite were used to create a label-free electrochemical biosensor for reliable Hcy detection. A novel Hcy-specific MIP (Hcy-MIP) was synthesized using methacrylic acid (MAA) in the presence of trimethylolpropane trimethacrylate (TRIM). The Hcy-MIP biosensor was fabricated by overlaying the mixture of Hcy-MIP and the carbon nanotube/chitosan/ionic liquid compound (CNT/CS/IL) nanocomposite on the surface of a screen-printed carbon electrode (SPCE). It showed high sensitivity, with a linear response of 5.0 to 150 µM (R2of 0.9753) and with a limit of detection (LOD) at 1.2 µM. It demonstrated low cross-reactivity with ascorbic acid, cysteine, and methionine. Recoveries of 91.10–95.83% were achieved when the Hcy-MIP biosensor was used for Hcy at 50–150 µM concentrations. The repeatability and reproducibility of the biosensor at the Hcy concentrations of 5.0 and 150 µM were very good, with coefficients of variation at 2.27–3.50% and 3.42–4.22%, respectively. This novel biosensor offers a new and effective method for Hcy assay compared with the chemiluminescent microparticle immunoassay at the correlation coefficient (R2) of 0.9946.