Patients undergoing allogeneic hematopoietic cell transplantation (alloHCT) experience a considerable decline in physical and psycho-social capacity. Since whole body vibration (WBV) is known to efficiently stimulate the neuromuscular system and enhance cardiorespiratory fitness and muscle strength in frail individuals, we hypothesized that WBV would maintain various physical and psychological capacities in patients during alloHCT. Seventy-one patients were randomly allocated to either an intervention group (IG) doing WBV or an active control group (CG) doing mobilization exercises five times per week. We determined peak oxygen consumption (VO 2peak) and maximum power, maximum strength, functional performance, body composition, quality of life (QoL), and fatigue. Tests were carried out before conditioning therapy, at hospital discharge and at day ± 180 (follow-up). As 18 patients did not participate in post-intervention assessment and follow-up data from 9 patients was not collectible, per-protocol (PP) analysis of 44 patients is presented. During hospitalization, WBV maintained maximum strength, height, and power output during jumping, as well as reported QoL, physical functioning, and fatigue level compared with mobilization. At follow-up, relative VO 2peak (p = 0.035) and maximum power (p = 0.011), time and power performing chairrising test (p = 0.022; p = 0.009), and reported physical functioning (p = 0.035) significantly increased in the IG, while fatigue decreased (p = 0.005). CG's body cell mass and phase angle had significantly decreased at follow-up (p = 0.002; p = 0.004). Thus, WBV might maintain maximum strength, functional performance, QoL, and fatigue during alloHCT, while cardiorespiratory fitness might benefit from accelerated recovery afterwards.