Background:We previously presented GraphVar as a user-friendly MATLAB toolbox for comprehensive graph analyses of functional brain connectivity. Here introduce a comprehensive extension of the toolbox allowing users to seamlessly explore easily customizable decoding models across functional connectivity measures as well as additional features.New Method: GraphVar 2.0 provides machine learning (ML) model construction, validation and exploration. Machine learning can be performed across any combination of graph measures and additional variables, allowing for a flexibility in neuroimaging applications.Results: In addition to previously integrated functionalities, such as network construction and graph-theoretical analyses of brain connectivity with a high-speed general linear model (GLM), users can now perform customizable ML across connectivity matrices, graph measures and additionally imported variables. The new extension also provides parametric and nonparametric testing of classifier and regressor performance, data export, figure generation and high quality export.Comparison with existing methods: Compared to other existing toolboxes, GraphVar 2.0 offers (1) comprehensive customization, (2) an all-in-one user friendly interface, (3) customizable model design and manual hyperparameter entry, (4) interactive results exploration and data export, (5) automated queue system for modelling multiple outcome variables within the same session, (6) an easy to follow introductory review.Conclusions: GraphVar 2.0 allows comprehensive, user-friendly exploration of encoding (GLM) and decoding (ML) modelling approaches on functional connectivity measures making big data neuroscience readily accessible to a broader audience of neuroimaging investigators.