Stifle injury is common in the companion dog population, affecting weight bearing, neuromuscular control, and balance. Therapeutic exercises after stifle injury seem to be effective, but high-quality research evaluating the effects is lacking. This randomized controlled trial evaluated the effects of a 12-week progressive therapeutic home exercise protocol on three-legged standing, targeting balance and postural- and neuromuscular control and disability in dogs with stifle injury. Thirty-three dogs with stifle injury were randomly allocated to intervention (n = 18) and control groups (n = 15), both receiving a standard rehabilitation protocol. Additionally, the intervention group received a progressive therapeutic exercise protocol. The outcome measures were static body weight distribution between hindlimbs, balance control, the canine brief pain inventory, and the Finnish canine stifle index. Both groups improved after the intervention period, but the group using the progressive therapeutic exercise protocol improved to a greater extent regarding static body weight distribution between the hindlimbs (I: median = 2.5%, IQR = 1.0–4.5; C: median = 5.5%, IQR = 3.0–8.8), pain-related functional disability (I: median = 0.0, IQR = 0.0–0.2; C: median = 0.9, IQR = 0.1–1.8), and stifle function (I: median = 25.0, IQR = 9.4–40.6; C: median = 75.0, IQR = 31.3–87.5), with intermediate to strong effects. These clinically relevant results indicate that this home exercise program can improve hindlimb function and restore neuromuscular control.