Factor Xa is the activated form of coagulation factor thrombokinase, also known as Stuart-Prower factor. Factor X is activated into factor Xa by factor IX (with factor VIII) and factor VII (with tissue factor). Factor Xa is inactivated by protein Z-dependent protease inhibitor (ZPI), a serine protease inhibitor (serpin).

The most commonly used anticoagulants in clinical practice, warfarin and the heparin series of anticoagulants, act to inhibit the action of Factor Xa.

Factor Xa protease can be used in biochemistry to cleave off protein tags that improve expression or purification of a protein of interest. Its preferred cleavage site (after the arginine in ile-glu/asp-gly-arg) can easily be engineered between a tag sequence and the protein. After expression and purification, the tag is then proteolytically removed by Factor Xa.