Virus detection methods based on nonlinear magnetic response of magnetic nanoparticles have been investigated, and magnetic detection methods using the third harmonic are widely applied, owing to their high sensitivity and short measurement time. This paper proposes a virus detection method based on the second harmonic because of its larger signal component. We found that the second harmonic signal is superior to the third harmonic signal for small nanobeads and a large change of the second harmonic signal in the signal-to-noise ratio (SNR) with nanobeads concentration. In addition, a virus detection limit of 100 pg/ml is achieved. Therefore, the proposed method can potentially be utilized for rapid screening of viruses.