The hybrid nanocomposite that consists of multiwalled carbon nanotubes (MWCNTs) and magnetite (Fe3O4) was fabricated by chemical co-precipitation method. Briefly, CNTs were oxidized with acids to form carboxylic group and then co-precipitated with Fe3O4 to form CNT–Fe3O4 nanocomposites. The nanocomposites were characterized by SEM, HRTEM, XRD, FTIR X-ray photoelectron spectrometry (XPS) and SQUID. The XRD results indicated the high crystallinity of Fe3O4 nanoparticles with spinel structure and the transmission electron microscope images depicted the intercalated iron oxide magnetic particles on the surface of CNTs. The MWCNTs–Fe3O4 was applied as a sensing interface to perform luminescence enzyme immunoassays. Firstly, EBNA-1 antigen was immobilized onto the carboxyl group functionalized MWCNTs–Fe3O4, followed by binding with anti-EBNA-1 IgA antibodies. The diluted secondary antibodies (anti-human IgA-HRP) were then added to the CNTs/Fe3O4–PEG–EBNA-1–anti-EBV IgA ab complex and act as a catalyst to produce a visible light upon reaction with the substrate luminol. The formed RLU is proportional to the amount of IgA anti-EBV antiobodies on the MWCNTs. The detection limit of proposed CNTs/Fe3O4 based luminescence enzyme immunoassay was in the order of 0.00128 EU/mL (1:100,000 fold dilution) for the detection of anti-EBV IgA antibodies, whereas the commercial ELISA and magnetic beads’ assay was accounted for up to the dilution fold of 1000 (i.e., 0.128 EU/mL). The initial findings showed that CNTs/Fe3O4 nanocomposites have a great potential in luminescent enzyme immunoassays and could be used as a sensing platform for the early screening of nasopharyngeal carcinoma.