A stent scaffold combined with amniotic tissue provides for a biocompatible stent that has improved biocompatibility and hemocompatibility. The amnion tissue can be variously modified or unmodified form of amnion tissue such as non-cryo amnion tissue, solubilized amnion tissue, amnion tissue fabric, chemically modified amnion tissue, amnion tissue treated with radiation, amnion tissue treated with heat, or a combination thereof. Materials such as polymer, placental tissue, pericardium tissue, small intestine submucosa can be used in combination with the amnion tissue. The amnion tissue can be attached to the inside, the outside, both inside and outside, or complete encapsulation of the stent scaffold. In some embodiments, at least part of the covering or lining comprises a plurality of layers of amnion tissue. The method of making the biocompatible stent and its delivery and deployment are also discussed.