A simple and rapid analytical method for thiabendazole (TBZ), imazalil (IMA), and o-phenylphenol (OPP) in citrus fruit has been developed by using flow-injection electrospray ionization tandem mass spectrometry for the first time. The method involves the combined use of stable isotopically labeled internal standards (thiabendazole-(13)C(6), imazalil-d(5), and p-phenylphenol-d(9)) and a multiple reaction monitoring technique. The average recoveries for the fungicides at the tolerance levels (TBZ and OPP, 10 mg/kg; IMA, 5 mg/kg) ranged from 77 to 101%, with the coefficients of variation (CVs) ranging from 0.7 to 4.2% (n = 5). At half the tolerance levels (TBZ and OPP, 5 mg/kg; IMA, 2.5 mg/kg), the average recoveries ranged from 62 to 112%, with the CVs ranging from 0.7 to 8.4% (n = 5). The CVs of the average recoveries, obtained from lemon samples fortified with three fungicides at the tolerance levels, obtained on three different days over two weeks, ranged within 2%. The analysis time, including sample preparation and determination, is only 15 min.