An enzyme-based electrochemical biosensor was fabricated for the sensitive determination of lactose. The utilized enzyme cascade system is composed of β-galactosidase (β-Gal) and glucose oxidase (GOx). The ruthenium(IV) oxide (RuO2) presents in MWCNT-RuO2 nanocomposite immobilized on the glassy carbon electrode acts as an electrochemical mediator, resembling a second-generation enzyme biosensor. The functional mechanism of the biosensor was discussed, explaining the chemical oxidation of H2O2, the final product of the enzymatic reaction, by RuO2 and subsequent reoxidation of generated Ru to RuO2 at the electrode surface. This shifts the oxidation of H2O2 to a lower potential magnitude of +0.40 V, enhancing the biosensor’s selectivity. The analytical figures of merit were verified for the developed lactose biosensor through repetitive measurements. The precision of the lactose biosensor was ensured with good reproducibility (RSD % = 2.68) and repeatability (RSD % = 4.12). The selectivity of the biosensor towards various saccharides and ionic species potentially present in milk samples was investigated, and no notable interference effect was detected. Moreover, the accuracy of the lactose biosensor was tested by analyzing spiked samples and a semi-skimmed milk (SS-milk) sample with certified lactose values. The limit of detection (LOD) and limit of quantification (LOQ) were calculated to be (0.036 mM) and (0.121 mM), respectively. Thanks to the short response time of the fabricated lactose biosensor, it was transferred to a screen-printed carbon electrode (SPCE) and successfully employed in flow injection analysis (FIA).