Hematopoietic stem cell transplantation (HSCT) requires a long hospitalization during which patients have to stay in transplantation wards, mainly in their single isolation rooms. One of the main goals of rehabilitation for HSCT patients is to prevent physical activity deficit by the introduction of an appropriate exercise programme and the monitoring of exercise adherence. The aim of our study was to evaluate the effectiveness of the prescribed exercise programme based on basic locomotor patterns to prevent physical activity deficit. The interim results of the prospective randomized controlled study included data from 20 patients. The study was approved by the Independent Ethics Committee and the Scientific Council of the 1Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology of Ministry of Healthcare of the Russian Federation. An experimental group included 11 patients aged 8–16 years old (the median age was 12 years old); a control group included 9 patients aged 5–11 years old (the median age was 8 years old). Patients from the experimental group were preliminarily taught a set of exercises aimed at practicing ontogenically determined standing up which they should further perform during a day in their isolation rooms. The control group patients received recommendations on how to maintain physical activity in their isolation rooms. Their physical activity during a day was then monitored by the researchers. All study subjects underwent an orthoclinostatic test (i.e., transition from lying to standing and back) for the evaluation of the autonomic nervous system function on Day 1 of pre-transplant conditioning therapy and at the time of discharge from the HSCT Department. During the entire stay at the HSCT Department, the patients from both groups were daily assessed using the ADL (activities of daily living) scale. At the time of discharge from the HSCT Department, the experimental group patients showed more adaptive autonomic nervous system responses than the control group patients. Our interim analysis showed that the patients from the experimental group had higher scores of activities of daily living than the control patients. Orthoclinostatic test results confirmed that patients undergoing HSCT for acute leukemia were predisposed to develop maladaptive conditions or even orthostatic hypotension. A set of exercises including those for the training of ontogenetically determined process of standing up was shown to be an effective tool for the prevention of insufficient autonomic nervous system responses. Even a short (30 min) face-to-face session with a physical therapist significantly increased a patient's daily physical activity.