Plant secondary metabolites with antioxidant properties, such as anthocyanins, are considered to have an important commercial value for some crops. Although anthocyanin concentration increases in response to various stimuli in plants, the mechanism of anthocyanin accumulation under multiple stimuli is not yet well understood. Here, we examined the effects of methyl jasmonate (MJ) and salinity on anthocyanin accumulation in radish (Raphanus sativus) sprouts. MJ treatments induced anthocyanin accumulation, which was enhanced by simultaneous treatment with salinity (200 mM NaCl), accompanied by growth restrictions. Sprouts treated with salinity alone did not induce anthocyanin accumulation, although sprout growth was restricted. Co-treatment with MJ and salinity increased hydrogen peroxide, total phenol content, and radical scavenging capacity more strongly than was achieved when each treatment was applied singly. Accumulation of anthocyanin was dependent on NaCl concentration and light intensity. Changing MJ and salinity treatment periods had different effects on anthocyanin accumulation and growth restriction, indicating that these phenomena might be differentially regulated. These results may provide an effective anthocyanin accumulation method without reducing plant biomass.