NeuroDOT, a MATLAB- and Python- based self-contained toolbox, addresses common challenges in processing of functional near infrared spectroscopy (fNIRS) and diffuse optical tomography (DOT) data. NeuroDOT supports multiple common pre-processing and analytical pipelines, including: simulation, data-anatomy alignment and modeling, pre-processing, data quality control, reconstruction, spectroscopy, post-processing, and extensive data visualizations at all stages of processing. We also provide pre-assembled, anonymized, and published data samples from our lab, chosen to reflect common experimental paradigms in neuroimaging including visual, language, and resting tasks for human brain mapping. Data are provided in both raw and pre-processed versions to aid in troubleshooting and training. Visualization and analysis tools provide powerful and intuitive explorations of data and data quality at every stage of processing and analysis. The latest release version of NeuroDOT is v1.2 (June 24, 2023).