Hand, Foot and Mouth Disease (HFMD) is a contagious viral disease caused by a group of enteroviruses, that frequently affects infants and children and present with blisters and flu-like symptoms. However, unlike other HFMD causing enteroviruses, EV71 have also been shown to be associated with more severe clinical manifestation leading to cardiopulmonary failure and death. Clinically, HFMD caused by EV71 is indistinguishable from other HFMD causing enteroviruses. Molecular diagnostics such as the use of real-time PCR has been commonly use for the identification of EV71. Despite the advances and the use of a highly established platform like the real-time PCR, challenges in viral load testing remains due to the intrinsic limitation of the methodology which central on the issue of precision, accuracy and standardisation. In this study, we utilise two platforms namely the real-time PCR and droplet digital PCR for the detection quantification of known EV71 viral copy number. The results reveal accurate and consistent results between the two platforms. The droplet digital PCR is therefore a promising technology for the identification and quantification of EV71 viral copy number.