Background and Objective: Heart rate variability (HRV) is an effective predictor of congestive heart failure (CHF). However, important challenges exist regarding the effective temporal feature extraction and efficient classification using high-dimensional HRV representations. To solve these challenges, an ensemble method for CHF detection using short-term HRV data and deep neural networks was proposed. Methods: In this study, five open-source databases, the BIDMC Congestive Heart Failure Database (BIDMC-CHF), Congestive Heart Failure RR Interval Database (CHF-RR), MIT-BIH Normal Sinus Rhythm (NSR) database, Fantasia database (FD) and Normal Sinus Rhythm RR Interval database (NSR-RR), were used. Additionally, three RR segment length types (N = 500, 1000 and 2000) were used to evaluate the proposed method. Firstly, we extracted the expert features of RR intervals (RRIs) and then built a long short-term memory-convolutional neural network-based network to extract deep-learning (DL) features automatically. Finally, an ensemble classifier was used for CHF detection using the above features. Results: With blindfold validation (three CHF subjects and three normal subjects), the proposed method achieved 99.85%, 99.41% and 99.17% accuracy on N = 500, 1000 and 2000 length RRIs, respectively, using the BIDMC-CHF, NSR and FD databases. With blindfold validation (six CHF subjects and six normal subjects), the proposed method achieved 83.84%, 87.54% and 85.71% accuracy on N = 500, 1000 and 2000 length RRIs, respectively, using the NSR-RR and CHF-RR databases. Based on feature ranking, the significant effectiveness provided by DL features has been proven. Conclusions: The results have shown that the deep ensemble method can achieve reliable CHF detection using short-term heart rate signals and enable the CHF detection through intelligent hardware.