Cooperative perception enabled by Vehicle-to-Everything (V2X) communication enhances autonomous driving safety by creating a unified environmental representation through shared sensory data. While recent works have advanced multi-agent fusion for improved perception, uncertainty quantification in such cooperative frameworks remains largely unexplored. This paper introduces Hyper-V2X, a hypernetwork-based framework for estimating both epistemic and aleatoric uncertainties in V2X-based perception. Specifically, we propose a partial weight generation scheme and V2X context embedding module that conditions a Bayesian hypernetwork on fused multi-agent features to generate weight distributions for stochastic Bird's-Eye-View (BEV) segmentation. Unlike existing deterministic BEV models, Hyper-V2X enables efficient uncertainty estimation with little computation overhead. Our approach is architecture-agnostic, and can be seamlessly integrating with modern cooperative backbones such as CoBEVT. Experiments on the OPV2V benchmark demonstrate that Hyper-V2X provides accurate, well-calibrated uncertainty estimates and improves overall perception reliability. Our code and benchmark are publicly available under an open-source license: https://github.com/abhishekjagtap1/Hyper-V2X

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