Purpose: We evaluate longitudinal changes in symptom clusters and core burdensome symptoms in breast cancer patients who participated in the OptiTrain trial. Methods: 240 women were randomized to 16 weeks of supervised exercise (RT-HIIT or AT-HIIT) or usual care (UC) during adjuvant chemotherapy. Symptom clusters were composed using the Memorial Symptom Assessment Scale (MSAS), assessed at baseline, 16 weeks and 12 months later. Three symptom clusters were formed. Results: Three symptom clusters were identified: "emotional," "treatment-related toxicity," and "physical," with core burdensome symptoms present over time. At 16 weeks, the reported burdens of "feeling sad" (RT-HIIT vs UC: effect size [ES] = -0.69; AT-HIIT vs UC: ES = -0.56) and "feeling irritable" (ES = -0.41 RT-HIIT; ES = -0.31 AT-HIIT) were significantly lower in both intervention groups compared with UC. At 12 months, the AT-HIIT group continued to have significantly lower scores for the core burdensome symptoms "feeling sad" (ES = -0.44), "feeling irritable" (ES = -0.44), and "changes in the way food tastes" (ES = -0.53) compared with UC. No between-group differences were found for physical symptoms. Conclusion: We identified 3 symptom clusters in breast cancer patients during and after adjuvant chemotherapy, composed of "emotional," "treatment-related toxicity," and "physical" symptoms. After treatment completion up to 12 months post-baseline, patients in the physical exercise groups reported lower symptom burden scores for emotional symptoms, compared with UC. Our findings indicate a preserved and long-term beneficial effect of physical exercise on self-reported emotional well-being in chemotherapy-treated breast cancer patients.