Federated Learning (FL) enables machine learning model training on distributed edge devices by aggregating local model updates rather than local data. However, privacy concerns arise as the FL server's access to local model updates can potentially reveal sensitive personal information by performing attacks like gradient inversion recovery. To address these concerns, privacypreserving methods, such as Homomorphic Encryption (HE)-based approaches, have been proposed. Despite HE's post-quantum security advantages, its applications suffer from impractical overheads. In this paper, we present FedML-HE, the first practical system for efficient HE-based secure federated aggregation that provides a user/device-friendly deployment platform. FedML-HE utilizes a novel universal overhead optimization scheme, significantly reducing both computation and communication overheads during deployment while providing customizable privacy guarantees. Our optimized system demonstrates considerable overhead reduction, particularly for large models (e.g., ∼10x reduction for HE-federated training of ResNet-50 and ∼40x reduction for BERT), demonstrating the potential for scalable HEbased FL deployment.