Mechanical forces play an important role in the initial stages of embryo development; yet, the influence of forces, particularly of tensile forces, on embryonic stem cell differentiation is still unknown. The effects of tensile forces on mouse embryonic stem cell (mESC) differentiation within a three-dimensional (3D) environment were examined using an advanced bioreactor system. Uniaxial static or dynamic stretch was applied on cell-embedded collagen constructs. Six-day-long cyclic stretching of the seeded constructs led to a fourfold increase in Brachyury (BRACH-T) expression, associated with the primitive streak phase in gastrulation, confirmed also by immunofluorescence staining. Further examination of gene expression characteristic of mESC differentiation and pluripotency, under the same conditions, revealed changes mostly related to mesodermal processes. Additionally, downregulation of genes related to pluripotency and stemness was observed. Cyclic stretching of the 3D constructs resulted in actin fiber alignment parallel to the stretching direction. BRACH-T expression decreased under cyclic stretching with addition of myosin II inhibitor. No significant changes in gene expression were observed when mESCs were first differentiated in the form of embryoid bodies and then exposed to cyclic stretching, suggesting that forces primarily influence nondifferentiated cells. Understanding the effects of forces on stem cell differentiation provides a means of controlling their differentiation for later use in regenerative medicine applications and sheds light on their involvement in embryogenesis.