Background: In the absence of randomized controlled trials (RCTs) on the benefits of therapeutic exercise programs involving children with bronchiectasis, we undertook a pilot RCT to evaluate the effects of a play-based therapeutic exercise program on fundamental movement skill (FMS) proficiency. The effects of the program on cardiorespiratory fitness, perceived competence, and health-related quality of life (HR-QoL) were examined as secondary outcomes. Methods: Children [median (IQR) age: 6.8 (5.3–8.8) years] with bronchiectasis unrelated to cystic fibrosis were randomized to a 7-week therapeutic exercise program (n = 11) or wait-list control (n = 10). The exercise program comprised 7 × 60-min weekly sessions and was supplemented by a home-based program 2-days/week. Participants were assessed on: FMS (locomotor and object control skills) using the Test of Gross Motor Development 2nd Edition (TGMD-2); cardiovascular fitness by calculating the percent change in heart rate (%ΔHR) from rest to completion of the first stage of a submaximal treadmill test; perceived competence using Harter’s athletic competence subscale; and QoL with the PedsQL. Results: Significant group by time interactions were observed for locomotor and object control skills. Children completing the therapeutic exercise program exhibited significant improvements in both locomotor (pre 29.0 ± 2.0, post 35.2 ± 2.2, p = 0.01) and object control (pre 27.0 ± 2.0, post 35.5 ± 2.2, p = 0.01) skills, with no significant change in controls (pre 31.6 ± 2.1, post 31.8 ± 2.3 and pre 31.0 ± 2.1, post 32.3 ± 2.3, respectively). Among children completing the program, %ΔHR declined by 6% points, while %ΔHR declined only marginally among controls (0.9% points), but the group by time interaction was not statistically significant. The program had a small positive impact on competence perceptions (Cohen’s d = 0.2) and HR-QoL (Cohen’s d = 0.3). Conclusion: This pilot RCT provides preliminary evidence for the efficacy of a play-based therapeutic exercise program to improve proficiency in FMS and fitness in children with bronchiectasis. The results are sufficiently positive to warrant conducting a larger RCT testing the efficacy of the exercise program in children with bronchiectasis and/or other chronic respiratory conditions.