Spinal cord fMRI data analysis involves niche pre- and post-processing steps due to the cord’s unique anatomy and higher distortions/physiological noise in fMRI data, requiring extensive and careful quality control (QC). However, there is paucity of open-source tools tailored to this need. Building upon 10 years of research and development, we present Neptune, a user-interface-based MATLAB toolbox. It can perform an array of tailored pre- and post-processing steps, including functional connectivity and statistics. It generates extensive QC plots and presents them to view in an elegant webpage format. We demonstrate the utility of Neptune on a 7T dataset.