Fast and reliable detection of viral infections is essential for effective disease control, early intervention, and the prevention of widespread outbreaks. In this context, we propose a homogeneous fluorescence-based assay using graphene quantum dots (GQDs) as a biosensing platform for the rapid and selective detection of viral nucleic acid sequences, demonstrated here with SARS-CoV-2 as a model target. A FAM-labelled single-stranded oligonucleotide, specific to the SARS-CoV-2 RdRP sequence, was immobilized onto the surface of GQDs via non-covalent interactions. We investigated the impact of surface oxygen functionalities on assay performance using three GQD variants: oxidized GQDs (GQD-Ox), carboxyl-functionalized GQDs (GQD-COOH), and hydroxyl-functionalized GQDs (GQD-OH). Upon hybridization with the complementary target, fluorescence quenching was observed, while negligible changes were seen with non-complementary and mutated sequences-confirming the assay's high selectivity. A strong linear correlation between fluorescence signal and target concentration was established across a wide dynamic range for all GQDs, with GQD-Ox exhibiting superior performance in terms of sensitivity, selectivity, linearity, and reproducibility. Importantly, the assay was finally optimized to reduce the target incubation time from 30 min to just 5 min, enabling the detection of SARS-CoV-2 sequences at concentrations as low as 139 pg/μL. These findings demonstrate the potential of GQD-Ox as a robust and efficient platform for the development of rapid, sensitive, and selective genosensors, with applicability not only to SARS-CoV-2 but also to other viral pathogens of clinical concern.