The displacement of soft tissues during activities such as running can influence athletic performance, according to previous research. Fatigue, on the other hand, is a condition that causes changes in running biomechanics. One strategy to reduce soft tissue displacement is the use of compression garments. This exploratory study aims to apply a novel methodology to quantify soft tissue displacement and analyse body shape changes during movement using dense 3D information of the body surface. Specifically, the study recruited one recreational runner to examine the effects of compression garments and fatigue on the lower limb during running. The technology used is MOVE4D (IBV, Valencia, Spain), which enables the analysis of variables such as thigh and calf perimeters and the Shape Variability Index. To assess the system’s reliability, the Intraclass Correlation Coefficient (ICC) was calculated under each experimental condition. The results show that the scanning system can distinguish between compression and no-compression conditions in the leg and provides consistent measurement of the running cycle. Additionally, fatigue was found to increase soft tissue movement, while the use of compression garments reduces soft tissue displacement in the lower limbs. The MOVE4D system emerges as an innovative, non-invasive technology for analysing soft tissue motion and presents a promising tool for the design of compression garments in sports applications.