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 104.55x 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.