Objective: This study proposes a novel deep learning approach for enhancing low-dose bone scintigraphy images using an Enhanced Convolutional Autoencoder (ECAE), aiming to reduce patient radiation exposure while preserving diagnostic quality, as assessed by both expert-based quantitative image metrics and qualitative evaluation. Methods: A supervised learning framework was developed using real-world paired low- and full-dose images from 105 patients. Data were acquired using standard clinical gamma cameras at the Nuclear Medicine Department of the University General Hospital of Alexandroupolis. The ECAE architecture integrates multiscale feature extraction, channel attention mechanisms, and efficient residual blocks to reconstruct high-quality images from low-dose inputs. The model was trained and validated using quantitative metrics—Peak Signal-to-Noise Ratio (PSNR) and Structural Similarity Index (SSIM)—alongside qualitative assessments by nuclear medicine experts. Results: The model achieved significant improvements in both PSNR and SSIM across all tested dose levels, particularly between 30% and 70% of the full dose. Expert evaluation confirmed enhanced visibility of anatomical structures, noise reduction, and preservation of diagnostic detail in denoised images. In blinded evaluations, denoised images were preferred over the original full-dose scans in 66% of all cases, and in 61% of cases within the 30–70% dose range. Conclusion: The proposed ECAE model effectively reconstructs high-quality bone scintigraphy images from substantially reduced-dose acquisitions. This approach supports dose reduction in nuclear medicine imaging while maintaining—or even enhancing—diagnostic confidence, offering practical benefits in patient safety, workflow efficiency, and environmental impact.