Background: Accurate and fast image registration (IR) is critical during surgical interventions where the ultrasound (US) modality is used for image-guided intervention. Convolutional neural network (CNN)-based IR methods have resulted in applications that respond faster than traditional iterative IR methods. However, general-purpose processors are unable to operate at the maximum speed possible for real-time CNN algorithms. Due to its reconfigurable structure and low power consumption, the field programmable gate array (FPGA) has gained prominence for accelerating the inference phase of CNN applications. Methods: This study proposes an FPGA-based ultrasound IR CNN (FUIR-CNN) to regress three rigid registration parameters from image pairs. To speed up the estimation process, the proposed design makes use of fixed-point data and parallel operations carried out by unrolling and pipelining techniques. Experiments were performed on three US datasets in real time using the xc7z020, and the xcku5p was also used during implementation. Results: The FUIR-CNN produced results for the inference phase 139 times faster than the software-based network while retaining a negligible drop in regression performance of under 200 MHz clock frequency. Conclusions: Comprehensive experimental results demonstrate that the proposed end-to-end FPGA-based accelerated CNN achieves a negligible loss, a high speed for registration parameters, less power when compared to the CPU, and the potential for real-time medical imaging.