Reliable extraction of structured data from radiology reports using Large Language Models (LLMs) remains challenging, especially for complex, non-English texts like Hebrew. This study introduces an agent-based uncertainty-aware approach to improve the trustworthiness of LLM predictions in medical applications. We analyzed 9,683 Hebrew radiology reports from Crohn's disease patients (from 2010 to 2023) across three medical centers. A subset of 512 reports was manually annotated for six gastrointestinal organs and 15 pathological findings, while the remaining reports were automatically annotated using HSMP-BERT. Structured data extraction was performed using Llama 3.1 (Llama 3-8b-instruct) with Bayesian Prompt Ensembles (BayesPE), which employed six semantically equivalent prompts to estimate uncertainty. An Agent-Based Decision Model integrated multiple prompt outputs into five confidence levels for calibrated uncertainty and was compared against three entropy-based models. Performance was evaluated using accuracy, F1 score, precision, recall, and Cohen's Kappa before and after filtering high-uncertainty cases. The agent-based model outperformed the baseline across all metrics, achieving an F1 score of 0.3967, recall of 0.6437, and Cohen's Kappa of 0.3006. After filtering high-uncertainty cases (greater than or equal to 0.5), the F1 score improved to 0.4787, and Kappa increased to 0.4258. Uncertainty histograms demonstrated clear separation between correct and incorrect predictions, with the agent-based model providing the most well-calibrated uncertainty estimates. By incorporating uncertainty-aware prompt ensembles and an agent-based decision model, this approach enhances the performance and reliability of LLMs in structured data extraction from radiology reports, offering a more interpretable and trustworthy solution for high-stakes medical applications.