This study aimed to modify screen-printed carbon micro-electrode surfaces by coating them with multiwall carbon-based nanotubes conjugated with chitosan and then validated the formed multiwall carbon-based nanotubes-chitosan coated screen printed carbon micro-electrode for the detection of homocysteine, a biomarker analyte known as a risk indicator in cardiovascular disease. The microstructure surface and crystallographic structure stability of the formed multiwall carbon-based nanotubes-chitosan obtained at formed multiwall carbon-based nanotubes per chitosan ratios of 1:1, 2:1, 3:1, and 4:1 were examined via field emission scanning electron microscopy, X-ray radiation, Raman spectroscopy, surface area and pore size, and thermogravimetric analyses. Homocysteine solutions at 30–100 µM were measured by cyclic voltammetry using the different formed multiwall carbon-based nanotubes-chitosan compositions as sensor electrodes. That with an optimal formed multiwall carbon-based nanotubes per chitosan ratio of 4:1 showed the highest crystallinity and electrical conductivity and gave a high coefficient of determination (R2 = 0.9036) between the homocysteine concentration and the oxidation current detection over an operating range of 30–100 µM. This new composite microelectrode for detecting homocysteine concentration makes it a promising candidate for clinical applications.