High-frequency oscillations (HFOs) are spontaneous magnetoencephalography (MEG) patterns that have been acknowledged as a putative biomarker to identify epileptic foci. Correct detection of HFOs in the MEG signals is crucial for the accurate and timely clinical evaluation. Since the visual examination of HFOs is time-consuming, error-prone, and with poor inter-reviewer reliability, an automatic HFOs detector is highly desirable in clinical practice. However, the existing approaches for HFOs detection may not be applicable for MEG signals with noisy background activity. Therefore, we employ the stacked sparse autoencoder (SSAE) and propose an SSAE-based MEG HFOs (SMO) detector to facilitate the clinical detection of HFOs. To the best of our knowledge, this is the first attempt to conduct HFOs detection in MEG using deep learning methods. After configuration optimization, our proposed SMO detector is outperformed other classic peermodels by achieving 89.9% in accuracy, 88.2% in sensitivity, and 91.6% in specificity. Furthermore, we have tested the performance consistency of ourmodel using various validation schemes. The distribution of performance metrics demonstrates that our model can achieve steady performance.