Transformer architectures for clinical prediction from electronic health records (EHRs) often require costly manual tuning and may vary across hospitals and tasks. We introduce ATHENA (Agentic Transfer across Hospitals for EHR Neural Architecture Search), a knowledge-guided agentic neural architecture search framework for Transformer-based EHR modeling. A weight-sharing supernet is pretrained once per hospital, allowing candidate architectures to inherit weights and be evaluated through fine-tuning rather than independent pretraining. A two-layer cross-hospital prior supplies high-performing source architecture examples and task-specific component preferences summarized by SHapley Additive exPlanations (SHAP)-based meta-regression. These priors guide a multi-agent large language model search using target-hospital validation feedback. Across six clinical prediction tasks at one held-out OneFlorida+ site and one external MIMIC-IV site, ATHENA significantly outperforms all four baselines in 9 of 12 site-task evaluations under a strict equal-compute comparison. In a separate comparison using a common pretrained AutoFormer supernet to isolate search strategy performance, ATHENA ranks first in 9 of 12 evaluations at a maximum search budget of 30 candidate evaluations. It also shows more consistent architecture selection across repeated searches. ATHENA supports more efficient architecture selection for Transformer-based clinical prediction models.

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