An automated system for on-line pre-concentration, separation and detection of plutonium in a urine sample was developed, based on the coupling of a multi-solvent delivery system, remotely-controlled switching modules, and an inductively coupled plasma mass spectrometer (ICP-MS). Effective separation between spectral and non-spectral interferences and Pu was performed viaTEVA selective extraction chromatography. Pu elution from the resin was performed using 0.01 M (NH4)2C2O4, directed to the ICP-MS through a switching module controlled by the multi-solvent delivery unit. The automated flow injection system (AFIS) enables the quantification of Pu isotopes for urinalysis at the sub-mBq L−1 range (DL: 0.21(239Pu), 0.19(240Pu) mBq L−1) in less than 15 min, with a chemical recovery exceeding 70%. The simplicity, speed, and automation of this approach make it attractive for radiological emergency response, especially considering its high daily sample throughput (>80). This throughput is the result of the faster flow rate used for the separation (up to 3 mL min−1) and the reusability of the extraction resin. If a calcium phosphate co-precipitation step is performed prior to loading the sample onto the TEVA resin, improvement in pre-concentration capacity is possible, making the AFIS usable for the assessment of occupational exposures.