Graph Neural Networks (GNNs) require a relatively large number of labeled nodes and a reliable/uncorrupted graph connectivity structure to obtain good performance on the semi-supervised node classification task. The performance of GNNs can degrade significantly as the number of labeled nodes decreases or the graph connectivity structure is corrupted by adversarial attacks or noise in data measurement/collection. Therefore, it is important to develop GNN models that are able to achieve good performance when there is limited supervision knowledge—a few labeled nodes and a noisy graph structure. In this paper, we propose a novel Dual GNN learning framework to address this challenging task. The proposed framework has two GNN based node prediction modules. The primary module uses the input graph structure to induce typical node embeddings and predictions with a regular GNN baseline, while the auxiliary module constructs a new graph structure through fine-grained spectral clustering and learns new node embeddings and predictions. By integrating the two modules in a dual GNN learning framework, we perform joint learning in an end-to-end fashion. This general framework can be applied on many GNN baseline models. The experimental results show that the proposed dual GNN framework can greatly outperform the GNN baseline methods and yield superior performance over many state-of-the-art methods when the labeled nodes are scarce and the graph connectivity structure is noisy.