Existing studies on relation extraction focus at the document level in a centralized training environment, requiring the collection of documents from various sources. However, this raises concerns about privacy protection, especially in sensitive domains such as finance and healthcare. For the first time, this work extends document-level relation extraction to a federated environment. The proposed federated framework, called FedLCC, is tailored for biomedical relation extraction that enables collaborative training without sharing raw medical texts. To fully exploit the models of all participating clients and improve the local training on individual clients, we propose a novel concept of localized context contrast on the basis of contrastive learning. By comparing and rectifying the similarity of localized context in documents between clients and the central server, the global model can better represent the documents on individual clients. Due to the lack of a widely accepted measure of non-IID text data, we introduce a novel non-IID scenario based on graph structural entropy. Experimental results on three document-level biomedical relation extraction datasets demonstrate the effectiveness of our method. Our code is available at https://github.com/xxxxyan/FedLCC.