Chronic Kidney Disease (CKD) affects over 850 million people globally, with early detection critical for effective intervention. We present DeepCKD-Net, a hybrid deep learning framework that synergistically integrates transformer architectures with gradient-boosting ensembles for multi-stage CKD prediction. Using a clinical dataset of 400 patients with 26 biomarker features from the UCI repository, our framework introduces three key innovations: (1) a hierarchical attention mechanism capturing complex inter-dependencies among clinical parameters, (2) an adaptive feature fusion module combining transformer-learned patterns with gradient-boosting decision boundaries, and (3) a confidence-aware ensemble strategy providing uncertainty quantification for clinical decision support. DeepCKD-Net achieves 98.7% accuracy and 0.993 AUC, surpassing state-of-the-art methods by 4.2% while maintaining 16.8 ms inference time suitable for real-time clinical deployment. Integrated SHAP analysis provides interpretable predictions, with serum creatinine (SHAP value: 0.342) and blood urea (0.287) identified as top predictive biomarkers, aligning with established clinical knowledge. The framework demonstrates robust performance under realistic clinical conditions, maintaining >90% accuracy with 20% missing data. Our contributions advance AI-driven nephrology diagnostics by providing a deployable, interpretable, and clinically validated solution for early CKD detection.