This paper reports a fast and sensitive method for early diagnosis of piscine nodavirus by using an automated microfluidic system. This system integrate a micro reverse transcription-polymerase chain reaction (RT-PCR) module, a capillary electrophoresis (CE) module, and buried optical fibers for on-line detection. The microfluidic chip is mainly fabricated from bio-compatible materials such as PDMS (polydimethylsiloxane), polymethylmethacrylate (PMMA), and soda-lime glass. With less human intervention, this integrated microfluidic device successfully detects the piscine nodavirus from clinical fish samples. Meanwhile, it shortens the detection time and also reduces the sample as well as reagent consumption. Moreover, the detection limit can be as low as 12.5 copies/μl by using the CE module. The experimental data confirm this integrated system could be a crucial tool for the diagnosis of RNA (ribonucleic acid)-based virus.