Noroviruses are the most frequent cause of foodborne viral gastroenteritis, causing approximately 90% of non-bacterial epidemic outbreaks around the world. Mulberry (Morus alba) seeds are by-products of juice and wine industries. Antiviral effects of mulberry seed extract (MAS) on foodborne viral surrogates, feline calicivirus-F9 (FCV-F9), and murine norovirus-1 (MNV-1) were evaluated by plaque assays and reverse transcription polymerase chain reaction. Polyphenol compound analysis using liquid chromatography-mass spectrometry revealed that caffeic acid, 3,4-dihydroxybenzoic acid, rutin, and cyanidin-3-rutinoside were the major compounds of MAS in a decreasing order. Its fraction (MAS-F1) with molecular weight less than 1 kDa, showed a similar composition, except for caffeic acid, a minor component. The maximal antiviral effect of FCV-F9 and MNV-1 was achieved when MAS or MAS-F1 was incubated with FCV-F9 and MNV-1 simultaneously added to cells. MAS-F1 further exhibited significant reduction of the MNV-1 or FCV-F9 polymerase gene expression in a dose-dependent manner. Among the polyphenols, cyanidin-3-rutinoside was effective in reducing MNV-1 polymerase gene expression. The inhibition of viral infection by MAS or MAS-F1 against foodborne viral surrogates may occur at the initial stage of viral replication.