An analytical method was developed for the identification and quantification of 15 mycotoxins (patulin, nivalenol, deoxynivalenol, aflatoxin B(1), B(2), G(1), G(2), M(1), T-2 toxin, HT-2 toxin, zearalenone, fumonisin B(1), B(2), B(3), and ochratoxin A) in beer-based drinks (beer, low-malt beer, new genre, and nonalcoholic) by a modified QuEChERS method and an ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC/MS/MS). Mycotoxins were extracted from samples using acetonitrile with sodium chloride, anhydrous magnesium sulfate, and sodium citrate, and were then purified with a solid phase extraction (SPE) cartridge including C18. The UHPLC conditions were also examined to establish its optimal conditions for separation. Fifteen mycotoxins were separated in a total of 6.5 min, and were quantified in the optimal mobile phase conditions. Determinations performed using this method produced high correlation coefficients of 15 mycotoxins (R>0.99) and recovery rates ranging from 70.3 to 110.7% with good repeatability (relative standard deviation RSD<14.6%). Further, 24 commercial beer-based drinks in Japan were analyzed using this method, and nivalenol, deoxynivalenol, and fumonisins were detected in several samples, but always under the limit of quantification (<5 ng/mL). These results suggest that the health risk to consumers from beer-based drinks in Japan is relatively low.