Geological CO2 sequestration (GCS) has been proposed as an effective approach to mitigate carbon emissions in the atmosphere. Uncertainty and sensitivity analysis of the fate of CO2 dynamics and storage are essential aspects of large-scale reservoir simulations. This work presents a rigorous machine learning-assisted (ML) workflow for the uncertainty and global sensitivity analysis of CO2 storage prediction in deep saline aquifers. The proposed workflow comprises three main steps: The first step concerns dataset generation, in which we identify the uncertainty parameters impacting CO2 flow and transport and then determine their corresponding ranges and distributions. The training data samples are generated by combining the Latin Hypercube Sampling (LHS) technique with high-resolution simulations. The second step involves ML model development based on a data-driven ML model, which is generated to map the nonlinear relationship between the input parameters and corresponding output interests from the previous step. We show that using Bayesian optimization significantly accelerates the tuning process of hyper-parameters, which is vastly superior to a traditional trial–error analysis. In the third step, uncertainty and global sensitivity analysis are performed using Monte Carlo simulations applied to the optimized surrogate. This step is performed to explore the time-dependent uncertainty propagation of model outputs. The key uncertainty parameters are then identified by calculating the Sobol indices based on the global sensitivity analysis. The proposed workflow is accurate and efficient and could be readily implemented in field-scale CO2 sequestration in deep saline aquifers.