Background: Earlier randomized controlled trials (RCTs) reported only midterm (3-4 months) results of extracorporeal shockwave therapy (ESWT) as a treatment for noninsertional Achilles tendinopathy (NAT). This study compared the effectiveness of an eccentric loading program followed by stretching exercises combined with ESWT (study group) or sham ESWT (control group) for treating chronic NAT in both the short and long term. Methods: This double-blind RCT was conducted between 2018 and 2020. Adult patients with unilateral NAT who failed standard conservative treatment were randomly allocated to either group. Function and pain were assessed at baseline, 1 month, and 16 months using the Victorian Institute of Sport Assessment–Achilles questionnaire (VISA-A) and visual analog scale (VAS), respectively. Mixed-design analysis of variance and nonparametric statistics were performed. Twenty-two men and 28 women aged 18 to 40 years were allocated into 2 equally matched groups. Results: Function and pain scores in the study group were not significantly different from control group scores at baseline (VISA-A: 22.2 ± 6.5 vs 21.0 ± 5.2 and VAS: 8 ± 1 vs 8 ± 1, respectively). Both groups significantly improved posttreatment (VISA-A: 85 ± 6.2 vs 53.4 ± 7.7 and VAS: 1 ± 2 vs 7 ± 2, respectively). At the 16-month follow-up, outcome scores declined slightly but significantly in the study group (VISA-A: 80 ± 5.3; VAS: 3 ± 2) and improved in the control group (VISA-A: 67 ± 5.6; VAS: 5 ± 1). However, both groups were significantly better than baseline. At both time points, the study group had significantly superior scores (statistically and clinically) than the control group ( P = .0001). Conclusions: Combining calf eccentric loading with stretching exercises resulted in significant improvements in the pain and functional scores in patients with NAT. Adding ESWT to this combined protocol resulted in significantly greater improvements in both the short and long term. Level of Evidence: Level I, randomized controlled trial.