Individual treatment effect (ITE) estimation is to evaluate the causal effects of treatment strategies on some important outcomes, which is a crucial problem in healthcare. Most existing ITE estimation methods are designed for centralized settings. However, in real-world clinical scenarios, the raw data are usually not shareable among hospitals due to the potential privacy and security risks, which makes the methods not applicable. In this work, we study the ITE estimation task in a federated setting, which allows us to harness the decentralized data from multiple hospitals. Due to the unavoidable confounding bias in the collected data, a model directly learned from it would be inaccurate. One well-known solution is Inverse Probability Treatment Weighting (IPTW), which uses the conditional probability of treatment given the covariates to re-weight each training example. Applying IPTW in a federated setting, however, is non-trivial. We found that even with a well-estimated conditional probability, the local model training step using each hospital's data alone would still suffer from confounding bias. To address this, we propose FED-IPTW, a novel algorithm to extend IPTW into a federated setting that enforces both global (over all the data) and local (within each hospital) decorrelation between covariates and treatments. We validated our approach on the task of comparing the treatment effects of mechanical ventilation on improving survival probability for patients with breadth difficulties in the intensive care unit (ICU). We conducted experiments on both synthetic and real-world eICU datasets and the results show that FED-IPTW outperform state-of-the-art methods on all the metrics on factual prediction and ITE estimation tasks, paving the way for personalized treatment strategy design in mechanical ventilation usage.