Abstract Background Previously, we have showed the 3-year clinical safety and efficacy of balloon expandable versus self-expandable stents in native coarctation of the aorta (CoA) in a randomized clinical trial (RCT). Very few prospective studies have addressed the changes of echocardiographic parameters in mid to long-term follow up of CoA patients treated endovascularly. Purpose We aimed to demonstrate the improvement of echocardiographic parameters among patients undergoing coarctoplasty with stent based on core laboratory-confirmed baseline and 3-year follow up transthoracic echocardiographic (TTE) images. Methods In the index RCT, adult patients with de novo native CoA were randomized into two groups based on stent types. All randomized patients received the 3-year structural follow-up including aortic CT angiography and TTE. The current prospective cohort substudy, included all patients with available baseline and three-year core laboratory TTEs. Results Of 92 patients initially randomized, 71 participated in the 3-year structural follow up. No baseline core lab images were available in 39 patients, and thus, 32 patients (a median age of 32 (24.8 – 37.5) years, (14 women [43.8%]) were included in this subgroup study. One out of the 32 patients presented with recoarctation which was successfully treated before the 3-year evaluation. Peak systolic gradient and end-systolic velocity of the coarctation stenting site were 17.38 ± 6.55 mmHg and 0.93 ± 0.24 m/s respectively in the 3-year follow-up. Septal E’ and lateral E’ velocities were improved significantly (8.6 ± 1.73 cm/s to 9.35 ± 2 cm/s, P = 0.02 and 12.74 ± 2.96 cm/s to 13.92 ± 2.44 cm/s, P = 0.03, respectively). In addition, septal E/E’ ratio (10.84 ± 2.83 to 9.21 ± 3.17, P = 0.02) and lateral E/E’ ratio (7.39 ± 2.24 to 6.29 ± 1.97, P = 0.02) showed significant improvement. Significant reduction in LV mass [160 (130–203) g to 142 (IQR= 121–172) g, P = 0.001], and septal and posterior LV thicknesses were also demonstrated (0.9 (0.8–1.0) cm to 0.81 (0.77–0.93) cm, P = 0.004) and 0.92 ± 0.14 cm to 0.85 ±0.09 cm, P = 0.01, respectively). Twelve (37.5%) patients had baseline LVH which was normalized in 9 (75%). Lastly, 12 (41.3%) of our population had diastolic dysfunction at baseline study which significantly decreased to 4 (13.7%) in the three-year follow-up evaluation. Conclusion In the present core laboratory-based study, coarctoplasty with stent has favorable effects on diastolic function and LV hypertrophy during midterm follow-up in adult population with de novo native aortic coarctation treated with stent.