Federated Learning (FL) is a beneficial decentralized learning approach for preserving the privacy of local datasets of distributed agents. However, the distributed property of FL and untrustworthy data introducing the vulnerability to backdoor attacks. In this attack scenario, an adversary manipulates its local data with a specific trigger and trains a malicious local model to implant the backdoor. During inference, the global model would misbehave for any input with the trigger to the attacker-chosen prediction. Most existing backdoor attacks against FL focus on bypassing defense mechanisms, without considering the inspection of model parameters on the server. These attacks are susceptible to detection through dynamic clustering based on model parameter similarity. Besides, current methods provide limited imperceptibility of their trigger in the spatial domain. To address these limitations, we propose a stealthy backdoor attack called “Chironex” against FL with an imperceptible trigger in frequency space to deliver attack effectiveness, stealthiness and robustness against various countermeasures on FL. We first design a frequency trigger function to generate an imperceptible frequency trigger to evade human inspection. Then we fully exploit the attacker’s advantage to enhance attack robustness by estimating benign updates and analyzing the impact of the backdoor on model parameters through a task-sensitive neuron searcher. It disguises malicious updates as benign ones by reducing the impact of backdoor neurons that greatly contribute to the backdoor task based on activation value, and encouraging them to update towards benign model parameters trained by the attacker. We conduct extensive experiments on various image classifiers with real-world datasets to provide empirical evidence that Chironex can evade the most recent robust FL aggregation algorithms, and further achieve a distinctly higher attack success rate than existing attacks, without undermining the utility of the global model.