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Federated learning (FL) is a promising privacy-preserving machine learning paradigm over distributed located data. In FL, the data is kept locally by each user. This protects the user privacy, but also makes the server difficult to verify data quality, especially if the data are correctly labeled. Training with corrupted labels is harmful to the federated learning task; however, little attention has been paid to FL in the case of label noise. In this paper, we focus on this problem and propose a learning-based reweighting approach to mitigate the effect of noisy labels in FL. More precisely, we tuned a weight for each training sample such that the learned model has optimal generalization performance over a validation set. More formally, the process can be formulated as a Federated Bilevel Optimization problem. Bilevel optimization problem is a type of optimization problem with two levels of entangled problems. The non-distributed bilevel problems have witnessed notable progress recently with new efficient algorithms. However, solving bilevel optimization problems under the Federated Learning setting is under-investigated. We identify that the high communication cost in hypergradient evaluation is the major bottleneck. So we propose \textit{Comm-FedBiO} to solve the general Federated Bilevel Optimization problems; more specifically, we propose two communication-efficient subroutines to estimate the hypergradient. Convergence analysis of the proposed algorithms is also provided. Finally, we apply the proposed algorithms to solve the noisy label problem. Our approach has shown superior performance on several real-world datasets compared to various baselines.