Purpose of research: Development of a complex physical therapy progam in association with transcranial magnetic stimulation at patients with ischemic stroke and assessing the effectiveness of its implementation in the recovery process. Materials and methods: The study was conducted on a sample of 32 patients hospitalized consecutively in the Department of Cerebrovascular Disease (CVD) of the National Scientific Practical Centre for emergency medicine in the period 2012-2013. The study included patients with the diagnosis of acute ischemic stroke, between the ages of 50-70 years. The lot was divided in two groups of 16 patients. For selecting patients and homogenisation of the groups were developed strict criteria for inclusion and exclusion in research. In the experimental group recovery was initiated within the first 24 hours after its debut, and the program included transcranial magnetic stimulation, respiratory gymnastics, positioning, stretching, passive mobilisation, orthotics and also were selected items from the proprioceptive neuromuscular facilitation and other approaches made by the Bobath, Brunnstrom and Rood. In the witness group of patients was applied classic program of recovery since the 2nd, 4th day from the debut. Results: The results of the study highlight the fact that kinetoterapeutic treatment initiated in the second or in the fourth day from debut, recorded a slower increase of the indices of assessment scales compared to the experimental group. Conclusions: Results of the study showed the success of the attempt to optimize the content of the recovery process for patients with ischemic stroke, which arises from the upper levels of indices at the experimental group compared to the witness group.