An effective flow injection analysis (FIA) system employing paired emitter detector diode (PEDD) for simultaneous dual antioxidant assays is proposed. The total antioxidant capacity (TAC) was measured using the 2,2′-azino-bis(3ethylbenzothiazoline-6-sulfonic acid) (ABTS) assay in parallel with the ferric reducing antioxidant power (FRAP) assay. Ascorbic acid was used as the reference antioxidant and the TAC value reported as ascorbic acid equivalent (AAE). A 10port valve furnished with two injection loops allowed the sample from one loop to react with the ABTS reagent and be detected by one PEDD. At the same time, the sample from the second loop reacted with the FRAP reagent and is detected at the second PEDD. A pair of red light emitting diodes (634 nm) was employed for both PEDDs. The linearity range was 10 to 50 μM ascorbic acid, with limit of detection of 3.18 and 4.37 μM, and precision of 2.41 and 2.15% RSD (for 30 μM ascorbic acid, n = 10) for the ABTS and FRAP assay, respectively. Sample throughput of 90 samples/h was achieved. The method was applied to the measurement of TAC of commercial fruit juice, instant tea products and vitamin C tablets. The observed AAE values were in good agreement with those obtained using batch methods with a spectrophotometer.