Aim: To develop high‐throughput screening (HTS) assays for monoamine oxidase (MAO)‐A and MAO‐B inhibitors. Methods: A fluorescence probe based method measuring MAO‐A and MAO‐B activity was established and optimized, with its sensitivity, stability and specificity evaluated. Reaction conditions including enzyme sources, substrate concentrations, incubation volume and reaction time in 384‐well format were optimized to achieve sensitive and low consumptive goal. Results: In optimized conditions, dynamic parameters of MAO‐A and MAO‐B were obtained. The Km value of serotonin to MAO‐A was 1.66 μmol/L, while that of benzylamine to MAO‐B was 0.80 μmol/L. The IC50 value of clorgyline to MAO‐A was 2.99 nmol/L, and that of deprenyl to MAO‐B was 7.04 nmol/L, matching those obtained from traditional spectrometric assays. Among tested samples, one compound exerted an inhibitory effect on MAO‐A activity with IC50 as 0.36 umol/L, and three compounds had an inhibitory effect on MAO‐B activity with IC50 as 0.13, 0.19, and 0.13 μmol/L. The Z′ factor was 0.71±0.03 and 0.75±0.03 in MAO‐A‐inhibitor and MAO‐B‐inhibitor HTS system, respectively. Conclusion: The established assays can be well applied to MAO‐A and MAO‐B inhibitor screening with high quality, precision and reproducibility.