In the field of structural health monitoring (SHM), vibration-based structural damage detection is an important technology to ensure the safety of civil structures. By taking advantage of deep learning, this study introduces a data-driven structural damage detection method that combines deep convolutional neural networks (DCNN) and fast Fourier transform (FFT). In this method, the structural vibration data are fed into FFT method to acquire frequency information reflecting structural conditions. Then, DCNN is utilized to automatically extract damage features from frequency information to identify structural damage conditions. To verify the effectiveness of the proposed method, FFT-DCNN is carried out on a three-story building structure and ASCE benchmark. The experimental result shows that the proposed method achieves high accuracy, compared with classic machine-learning algorithms such as support vector machine (SVM), random forest (RF), K-Nearest Neighbor (KNN), and eXtreme Gradient boosting (xgboost).