A dual channel chemiluminescence FIA system for the rapid measurement of the fish freshness index KI where [IMP], [HxR] and [Hx] are, respectively, the inosine 5′-monophosphate, inosine and hypoxanthine contents of fish meat was developed. The system consisted of a pair of chemiluminescence FIAs (CL-FIA); one for the measurement of [IMP] + [HxR] + [Hx], and the other for [HxR] + [Hx]. IMP, HxR or Hx were measured using a reactor comprising immobilized alkaline phosphatase, purine nucleoside phosphorylase (PNP) and xanthine oxidase (XOD). The calibration curves for IMP, HxR or Hx were linear from 0.06 μM to 100 μM for a sample volume of 20 μl. The time for a single KI measurement was less than 1 min. This fish freshness FIA system is rapid, convenient and applicable for fish freshness measurements in real fish samples.