Methotrexate (MTX) is a chemotherapy agent and immune system suppressant that is widely used to treat a variety of malignant and nonmalignant diseases. Due to some drawbacks of the existing methods for the determination of MTX in aquatic and real samples, we prepared a new, simple, and selective dual‐mode fluorometric and electrochemical approach based on peroxidase‐mimic [Mo36] polyoxomolybdate nanoclusters (POMo) for sensing MTX. A turn‐on–off fluorometric approach for the detection of MTX was developed, which was based on the inhibition of the emission intensity of the terephthalic acid (TA)‐H2O2 system upon the addition of MTX to the reaction solution. The electrocatalytic performance of the obtained POMo was studied after making a carbon paste electrode (CPE) utilizing cyclic voltammetry and amperometry analysis. Under the optimum condition, good linearity was observed between the quenched emission intensity of the system and MTX dosage in the range of 0.5–250 μM with a limit of detection (LOD) of 0.91 μM. The electrochemical method illustrated a much better response with an extensive linear range of 0.01–475 μM and a lower LOD (1.61 nM). Analytical recoveries and RSD% values were, respectively, in the range of 87.72%–110% and 0.33%–1.32% for the fluorometric system and 96%–106% and 0.77%–1.02% for the electrochemical platform. Finally, the selectivity of the sensor was evaluated against various common interfering species, and the results indicated satisfactory selectivity of the POMo dual‐mode system towards MTX.