Hepatitis C virus (HCV) NS5A protein plays essential roles in both RNA replication and virion assembly at the surface of cytoplasmic lipid droplets (LDs), although the precise mechanisms are unclear. In previous work we have shown that tagging NS5A with a tetracysteine (TCM) motif (Jc1/5A-TCM) and visualising NS5A traffic in a productive infection results in two distinct NS5A populations: one static and one highly motile, although the role and composition of these structures is not well understood. To address if NS5A motile structures contain HCV RNA we developed a system to simultaneously track HCV RNA and NS5A in living cells. MS2 bacteriophage RNA stem loop sequences (24x) were inserted into the 3’UTR of Jc1/5A-TCM (Jc1/NS5A-TCM:MS2) virus to allow indirect tracking of HCV RNA in Huh-7.5 cells via mCherry-tagged MS2 Coat protein that interacts specifically with MS2 stem loops. Jc1/NS5a-TCM:MS2 replicated to significantly lower levels than its parent as assessed by infectivity assays (FFA) and immunofluorescence analysis. However, long-term culture resulted in emergence of viral replication, with partial retention of MS2 stem loops at 8 days post electroporation. Most importantly, in these cultures there was a redistribution of the mCherry tagged MS2 coat protein from a homogenous cytoplasmic distribution to a punctate staining pattern indicative to specific binding to HCV RNA. Using this approach we have simultaneously visualised HCV RNA (MS2coat-mCherry) and NS5A traffic (FlAsH) in real-time during HCV replication. Interestingly, both NS5A small motile and larger static structures were found to be enriched with HCV RNA. We also investigated viral RNA traffic with respect to the lipid droplet (LD) and show that both NS5A static and motile NS5A enriched structures dynamically interact with the LD consistent with their role as sites for RNA replication and delivery of HCV RNA to the site of virion assembly.