The detection of bioactive nanoparticles (NPs) plays an important role in the medical and diagnostic fields. Conventional techniques for the sensitive detection of target NPs must overcome challenges such as long processing time, complex sample preparation, and high cost. Here, we show that vibration-induced flow (VIF), in which a local flow is induced around microscopic objects by applying small periodic vibrations, can be used to realize rapid, facile, highly sensitive, and low-cost detection of NPs in a minute sample. In the proposed system, the presence of NPs in a sample is detected by the formation of aggregates of affinity capture beads stirred by the VIF within a short time (approximately 15 min). Furthermore, the concentration of NPs can be quantified using the average area of the aggregate observed in bright-field microscopic images without using an expensive image analyzer and fluorescence labeling of targets, which are commonly used in other NP detection protocols. Finally, we demonstrate the detection of extracellular vesicles (EVs) to validate the applicability of the proposed system in diagnostic applications.