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Kidney diseases, whether acute or chronic, remain among the most challenging conditions to diagnose due to their complex and often asymptomatic progression. Emerging biomarkers such as neutrophil gelatinase-associated lipocalin (NGAL) and cystatin C (CysC) correlate with early pathogenesis and offer complementary insights into disease etiology. However, quantification of their levels, which is essential for patient staging, is available only in centralized laboratories. We present the lateral-flow microfluidic bead-based assay (LMBA), the first rapid, self-contained system for NGAL and CysC analysis. LMBA integrates a microfluidic chip with paper-based components to run automated high-resolution immunoassays in 20 min. Its modular architecture, decoupling reagent storage and flow control from assay binding and readout, offers significant design flexibility. Validated against ELISA, LMBA exhibits comparable sensitivity with an extended dynamic range, requiring only 1 μL of the original blood or urine sample prior to dilution. We applied the LMBA to neonatal mouse models of polycystic kidney disease and measured biomarker elevations consistent with cyst progression. This scalable platform supports preclinical research and holds strong potential for decentralized kidney disease diagnostics.