Challenging HR conditions, such as elevated Heart Rate (HR) and Heart Rate Variability (HRV), are major contributors to motion artifacts in Coronary Computed Tomography Angiography (CCTA). This study aims to assess the impact of a deep learning-based motion correction algorithm (MCA) on motion artifacts in patients with challenging HR conditions, focusing on image quality and diagnostic performance of CCTA. This retrospective study included 240 patients (mean HR: 88.1 ± 14.5 bpm; mean HRV: 32.6 ± 45.5 bpm) who underwent CCTA between June, 2020 and December, 2020. CCTA images were reconstructed with and without the MCA. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were measured to assess objective image quality. Subjective image quality was evaluated by two radiologists using a 5-point scale regarding vessel visualization, diagnostic confidence, and overall image quality. Moreover, all vessels with scores ≥ 3 were considered clinically interpretable. The diagnostic performance of CCTA with and without MCA for detecting significant stenosis (≥ 50%) was assessed in 34 patients at both per-vessel and per-patient levels, using invasive coronary angiography as the reference standard. The MCA significantly improved subjective image quality, increasing the vessel interpretability from 89.9% (CI: 0.88-0.92) to 98.8% (CI: 0.98-0.99) (p < 0.001). The use of MCA resulted in significantly higher diagnostic performance in both patient-based (AUC: 0.83 vs. 0.58, p = 0.04) and vessel-based (AUC: 0.92 vs. 0.81, p < 0.001) analyses, with the vessel-based accuracy notably increased from 79.4% (CI: 0.72-0.86) to 91.2% (CI: 0.85-0.95) (p = 0.01). There were no significant differences in objective image quality between the two reconstructions. The mean effective dose in this study was 2.8 ± 1.1 mSv. The use of MCA allows for obtaining high-quality CCTA images and superior diagnostic performance with low radiation exposure in patients with elevated HR and HRV.