The present invention relates to a fluorescence-based detection system and method for detecting DENV RNA in patient''s serum directly. This is a rapid method and does not require any nucleic acid amplification step and can precisely detect dengue RNA within two hours confirming ongoing DENV replication in the patient. The method uses complementary sequence in the molecular probe which would specifically bind to conserved target sequence of DENV RNA in the infected serum samples. The molecular probes are approximately 37-40 bases long hairpin structures (stem and a loop) with a fluorophore-quencher system attached at the terminal end of the stem. These probes are biotinylated in the stem region so that they can be immobilized to the streptavidin-tagged magnetic beads.