Massive volumes of data are needed for deep learning (DL) models to provide accurate diagnosis results. Numerous studies of fault diagnosis systems have demonstrated the effectiveness of DL models over shallow machine learning (SL) in terms of feature extraction, feature dimensional reduction and diagnosis performance. Occasionally, during data acquisition, a problem with a sensor renders some of the data potentially unsuitable for further analysis, leaving only a small data sample. To compensate for this deficiency, a DL model based on a stacked sparse autoencoder (SSAE) model is designed to deal with limited sample data. In this article, the fault diagnosis system is developed based on time-frequency image pattern recognition. Therefore, two gearbox datasets are used to evaluate the proposed diagnosis system. The results from the experiments prove that the proposed system is capable of achieving high diagnostic accuracy even with limited sample data. The proposed fault diagnosis system achieved 100% and 99% diagnosis performance on experimental gearbox and wind turbine gearbox datasets, respectively. The proposed diagnosis system increased diagnosis performance between 10% and 20% over the standard SSAE model. In addition, the proposed model achieved higher diagnosis performance compared to deep neural network and convolutional neural networks models.