Convolutional Neural Networks (CNNs) represent the cutting edge in signal analysis tasks like classification and regression. Realization of such architectures in hardware capable of performing high throughput computations, with minimal energy consumption, is a key enabling factor towards the proliferation of analysis immediately after acquisition. Our driving problem is a satellite-based remote sensing platform in which onboard signal processing and classification tasks must take place, given strict bandwidth and energy limitations. In this work, we exploit the implementation of a CNN on Field Programmable Gate Array (FPGA) platforms and explore different ways to minimize the impact of different hardware restrictions to performance. We compare our results against competing technologies such as Graphics Processing Units (GPU) in terms of throughput, latency and energy consumption. In actual experimental runs we demonstrate competitive latency and throughput of the FPGA platform vs. GPU technology at an order-of-magnitude energy savings, which is especially important for space-borne computing.