The methodology for the rapid determination of 89,90Sr in wide range of activity concentration is given. Methodology is based on simultaneous separation of strontium and yttrium from samples by mixed solvent anion exchange chromatography, mutual separation of 89,90Sr from 90Y by hydroxide precipitation and quantitative 89,90Sr determination by Cherenkov counting within 3 days. It is shown that Y and Sr can be efficiently separated from alkaline, alkaline earth and transition elements as well as from lanthanides and actinides on the column filed by strong base anion exchanger in nitrate form and 0.25 M HNO3 in mixture of ethanol and methanol as eluent. Decontamination factor for Ba, La and other examined elements except calcium is low and can not affect quantitative determination in predictable circumstances. Methodology for quantitative determination by Cherenkov counting based on following the changes of sample activity over time is described and discussed. It has been shown that 89,90Sr can be determined with acceptable accuracy when 89Sr/90Sr ratio is over 10:1 and that separation of Y enables reliable determination of 89Sr and 90Sr in wide range of 89Sr/90Sr ratios (60:1) and in some cases in presence of other yttrium and strontium isotopes. The methodology was tested by determination of 89,90Sr in Analytics crosscheck samples (nuclear waste sample) and ERA proficiency testing samples (low level activity samples). Obtained results shows that by using of low level liquid scintillation counter it can be possible to determine 89Sr and 90Sr in wide range of concentration activity (1–1,000 Bq/L/kg) with uncertainty below 10% within 2–3 days. Results also show that accuracy of determination of 89Sr (and 90Sr) strongly depends on the determination of difference between separation and counting time when activity ratio of 89Sr/90Sr is high. Examination the influence of media and vial type on background radiation and counting efficiency has shown that lowest limit of determination can be obtained by using of HNO3 in plastic vials as counting media, because in this combination figure of merit is maximized. For the recovery of 50% and 100 min of counting time estimated MDA is 55 Bq and 90 Bq for 90Sr and 89Sr, respectively. Analysis of combined uncertainty shows that it mainly depends on uncertainty of efficiency and recovery determination, uncertainty of activities determination for both isotopes and level of background radiation.