A rapid, simple, improved method for the simultaneous determination of patulin (PAT) and 5-hydroxymethylfurfural (5-HMF) in fruit juices is described. The target compounds were extracted with ethyl acetate using vortex followed by high performance liquid chromatographic separation. PAT and 5-HMF were separated within 4 min using Poroshell C18 column with acetonitrile:water (1:9, v/v) as the mobile phase. Under the optimized conditions, the detection limits of PAT and 5-HMF were 0.25 and 0.46 ng mL −1 , respectively while the quantification limits were 0.76 and 1.40 ng mL −1 , respectively. The recoveries of PAT and 5-HMF at 50, 750 and 5000 ng g −1 ranged from 92.8 to 108%. The proposed method was applied to fivety-six fruit juices (apple, mango, pineapple, guava, lychee, tamarind, soursop and mixed fruit) and PAT was found in three samples ranging from 13.1–33.7 ug L −1 . 5-HMF was found in all the samples ranging from 0.08 to 91.5 mg L −1 . Liquid chromatography-tandem mass spectrometry with triple quadrupole analyzer was used to confirm the presence of 5-HMF and PAT in some of the contaminated samples.