An automated procedure for the determination of (99)Tc in aged nuclear waste has been developed. Using advanced sequential injection (SI) analysis instrumentation, (99)Tc(VII) is separated from radioactive and stable interferences using a TEVA resin column that selectively retains pertechnetate ion from dilute nitric acid solutions. The separated (99)Tc is eluted with 6 M nitric acid and quantified on-line with a flow-through liquid scintillation detector. A stopped-flow technique has been optimized that improves the analysis precision and detection limit compared to continuous-flow detection, reduces consumption of liquid scintillation cocktail, and increases sample throughput by separating the next sample while the present sample is being counted. The detection limit is 30 pCi, or 2 ng, of (99)Tc, using a 15-min stopped-flow period. The analysis time is 40 min for the first sample and is reduced to 20 min for each subsequent sample. Processed nuclear waste samples from the Hanford site were successfully analyzed by this new method.