Fast-scan cyclic voltammetry (FSCV) is an electrochemical technique for measuring rapid changes in the extracellular concentration of neurotransmitters within the brain. Due to its fast scan rate and large output-data size, the current analysis of the FSCV data is often conducted on a computer external to the FSCV device. Moreover, the analysis is semi-automated and requires a good understanding of the characteristics of the underlying chemistry to interpret, making it unsuitable for real-time implementation on low-resource FSCV devices. This paper presents a hardware-software co-design approach for the analysis of FSCV data. Firstly, a deep neural network (DNN) is developed to predict the concentration of a dopamine solution and identify the data recording electrode. Secondly, the DNN is pruned to decrease its computation complexity, and a custom overlay is developed to implement the pruned DNN on a low-resource FPGA-based platform. The pruned DNN attains a recognition accuracy of 97.2% with a compression ratio of 3.18. When the DNN overlay is implemented on a PYNQ-Z2 platform, it achieves the execution time of 13 ms and power consumption of 1.479 W on the entire PYNQ-Z2 board. This study demonstrates the possibility of operating the DNN for FSCV data analysis on portable FPGA-based platforms.