Lipocalin-2 (Lcn2) is a biomarker for many inflammatory-based diseases, including acute kidney injury, cardiovascular stress, diabetes, and various cancers. Inflammatory transitions occur rapidly in kidney and cardiovascular disease, for which an in-line monitor could be beneficial. Microcantilever devices with aptamers as recognition elements can be effective and rapidly responsive sensors. Here, we have selected and characterized an RNA aptamer that specifically binds mouse Lcn2 (mLcn2) with a dissociation constant of 340 ± 70 nM in solution and 38 ± 22 nM when immobilized on a surface. The higher apparent affinity of the immobilized aptamer may result from its effective multivalency that decreases the off-rate. The aptamer competes with a catechol iron-siderophore, the natural ligand of mLcn2. This and the results of studies with mLcn2 mutants demonstrate that the aptamer binds to the siderophore binding pocket of the protein. A differential interferometer-based microcantilever sensor was developed with the aptamer as the recognition element in which the differential response between two adjacent cantilevers (a sensing/reference pair) is utilized to detect the binding between mLcn2 and the aptamer, ensuring that sensor response is independent of environmental influences, distance between sensing surface and detector and nonspecific binding. The system showed a detection limit of 4 nM. This novel microcantilever aptasensor has potential for development as an in-line monitoring system for mLcn2 in studies of animal models of acute diseases such as kidney and cardiac failure.