Background: The aim of this study was to assess if thermography as an objective and non-invasive research tool is capable of identifying the changes in the surface temperature of the body as a response to muscle stimulation in Vojta therapy. The research group consisted of children aged 3–10 months with slight abnormalities of the motor pattern, subjected to individually selected stimulation elements according to Vojta. Methods: The Vojta method of spontaneous motor assessment and the thermovision method of assessing the microcirculation properties of muscles were used for the evaluation. Results: In the study group, changes in the microcirculation parameters of the extensor muscles of the back occurred immediately after the therapy at the first examination. Conclusions: The analysis featuring an objective assessment allows physiotherapists to diagnose local temperature changes based on the effect of microcirculation parameters in the musculofascial structures. Trial registration: The research was conducted as a pilot study for a scientific project approved by the Commission for Scientific Research of the University of Health and Sport Sciences in Wroclaw No 24/2021. The study is currently in the registration process with the Australian New Zealand Clinical Trials Registry.