Due to the dramatic increase of data volume in modern high energy physics (HEP) experiments, a robust high-speed data acquisition (DAQ) system is very much needed to gather the data generated during different nuclear interactions. As the DAQ works under harsh radiation environment, there is a fair chance of data corruption due to various energetic particles like alpha, beta, or neutron. Hence, a major challenge in the development of DAQ in the HEP experiment is to establish an error resilient communication system between front-end sensors or detectors and back-end data processing computing nodes. Here, we have implemented the DAQ using field-programmable gate array (FPGA) due to some of its inherent advantages over the application-specific integrated circuit. A novel orthogonal concatenated code and cyclic redundancy check (CRC) have been used to mitigate the effects of data corruption in the user data. Scrubbing with a 32-b CRC has been used against error in the configuration memory of FPGA. Data from front-end sensors will reach to the back-end processing nodes through multiple stages that may add an uncertain amount of delay to the different data packets. We have also proposed a novel memory management algorithm that helps to process the data at the back-end computing nodes removing the added path delays. To the best of our knowledge, the proposed FPGA-based DAQ utilizing optical link with channel coding and efficient memory management modules can be considered as first of its kind. Performance estimation of the implemented DAQ system is done based on resource utilization, bit error rate, efficiency, and robustness to radiation. © 1963-2012 IEEE.