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Many machine learning applications require outputs that satisfy complex, dynamic constraints. This task is particularly challenging in Graph Neural Network models due to the variable output sizes of graph-structured data. In this paper, we introduce ProjNet, a Graph Neural Network framework which satisfies input-dependant constraints. ProjNet combines a sparse vector clipping method with the Component-Averaged Dykstra (CAD) algorithm, an iterative scheme for solving the best-approximation problem. We establish a convergence result for CAD and develop a GPU-accelerated implementation capable of handling large-scale inputs efficiently. To enable end-to-end training, we introduce a surrogate gradient for CAD that is both computationally efficient and better suited for optimization than the exact gradient. We validate ProjNet on four classes of constrained optimisation problems: linear programming, two classes of non-convex quadratic programs, and radio transmit power optimization, demonstrating its effectiveness across diverse problem settings.