Purpose Patients undergoing allogeneic hematopoietic cell transplantation (alloHCT) spend many weeks of treatment in an isolated environment with little room for exercise. Feasibility of a daily-performed, unassisted fascia-training program and its effects on back and foot pain, back flexibility, and quality of life were investigated. Methods Eighteen patients receiving alloHCT were randomized to an intervention (IG: n = 9; 60.7 ± 9.2 years) or control group (CG: n = 9; 54.0 ± 15.5 years) and assessed from 1 week before to 3 weeks after transplantation (t0–t3). CG received standard care physical therapy, IG performed additionally fascia training for the back and feet twice daily. Back and foot pain, back flexibility, muscle tone, and quality of life were assessed for both IG and CG at baseline and three timepoints after alloHCT. Results Fascia-training program was well accepted. No increase in hematoma formation was observed. IG reported a trend towards reduction in back pain from pre- to post-intervention (p = .074), whereas CG showed a slight increase in back pain at t3 (p = .257). IG also improved back flexibility (− 1.79 ± 5.5 cm; p = .397) while CG declined (+ 2.71 ± 5.6 cm; p = .167). No differences between groups were found for muscle tone and no significant improvements in quality of life were reported at t3. Conclusion Unassisted fascia training is feasible and safe for patients undergoing alloHCT. This pilot study suggests that fascia training has the potential to improve back flexibility and reduce back pain, and might be a valuable component for physical therapy in patients receiving alloHCT.