Successful diagnosis and treatment of many diseases depends on the availability of sensitive, reliable and low cost tools for the detection of the biomarkers associated with the diseases. Simple methods that use non-invasive biological samples are especially suitable for the deployment in the clinical environment. In this paper we demonstrate the application of a method that employs a capped gold nanoslit surface plasmon resonance (SPR) sensor and a microfluidic chip for the detection of a urinary nucleic acid biomarker in clinical samples. This method detects low concentrations of the biomarker in a relatively large volume (∼1 mL) of the sample. The method utilizes magnetic nanoparticles (MNPs) for the isolation of target molecules and signal enhancement in conjunction with surface plasmon resonance (SPR) on capped gold nanoslits. The ability of the method to detect urinary miRNA-16-5p in AKI patients was tested and the result was compared with the data obtained with the polymerase chain reaction (PCR). miRNA-16-5p has been found to be a specific and noninvasive biomarker for acute kidney injury (AKI). Our method allows the detection of the biomarker in the urine of AKI patients without amplification and labeling of the target molecules.