Hepatitis C is a public health problem worldwide, affecting chronically about 71 million people, or 1% of the world population. The early detection of infection in clinical practice routine and blood donors is still important, being necessary for the development of new specific, sensitive, reliable tests that can improve the screening of HCV infection. Flow cytometry beads assay opens the possibility to detect multiple antigens, decrease cross-reactivity, increase in the sensitivity, with low sample volumes. Here, we describe proof-of-concept of a method for anti-Core and anti-NS5a detection using magnetic beads and flow cytometry. The immunoassay presented 93.33% sensitivity and 100% specificity for rCore magnetic beads (MgBs), and 93.33% sensitivity and 96.67% specificity for rctNS5a MgBs. The accuracy values for the tests using rCore and rctNS5a MgBs were 96.67% and 95%, respectively. The results of the ROC curve were 0.97 and 0.99 for rCore and rctNS5a MgBs, respectively. Therefore, we concluded that the method presented here for the detection of anti-HCV antibodies using magnetic beads analyzed by flow cytometry showed promising results, achieving satisfactory sensitivity and specificity values, with future potential to be an alternative method for screening anti-HCV antibodies in blood banks and blood centers.