Hepatitis A virus (HAV) infection leads to acute liver failure and death through the intake of contaminated food. The polymerase chain reaction (PCR) has been used to detect HAV in food samples. HAV detection takes a long time, however, due to the virus concentration step required before PCR assay. In this study, a rapid method of detecting the HAVs present in lettuce using immunomagnetic separation combined with quantum dots (IMS-QDs) assay was developed. The detection limit of IMS-QDs for HAV was 10 TCID50/mL, similar to the result that was obtained using RT-PCR combined with PEG or IMS. The application of IMS-QDs assay completed the viral detection within one hour, but this was not possible using PEG combined with RT-PCR. In conclusion, IMS-QDs assay is a rapid and efficient method for detecting HAV at a low concentration in agricultural products.