The efficacy and effectiveness of Convolutional Neural Networks (CNNs) have been proven in a wide range of machine learning applications. However, the high computational complexity of CNNs presents a critical challenge towards their broader adoption in real-time and power-efficient scenarios. FPGAs are poised to take a significant role for high-performance and energy-efficient computation of CNNs for both mobile (e.g., UAVs, self-driving cars, and IoT devices) and cloud computing domains. However, implementing an effective CNN system onto FPGAs efficiently remains problematic. The current cloud-based FPGAs with unique design constraints and architectural characteristics further increase the challenges. To address these challenges, we propose a novel open-source automated tool chain called Cloud-DNN. Our tool chain takes trained CNN models specified in Caffe as input, performs a set of transformations, and maps the model to a cloud-based FPGA. Cloud-DNN can significantly improve the overall design productivity of CNNs on FPGAs while satisfying the emergent computational requirements. Our design provides an alternative solution compared to other cloud-based options (e.g., GPUs or TPUs) while offering flexible, and high performance DNN inferences. The unique features of Cloud-DNN include the optimizations with cloud-platform characteristics and the support of easier and streamlined implementation. Experimental results demonstrate up to 104.55× performance improvement when compared to CPU implementation and comparable usability, flexibility, and strong quality compared to other state-of-the-art DNN inference implementations on standalone FPGAs.