The reliable stress intensity factor analysis is required for fracture mechanics design or safety evaluation of mechanical joints at which cracks often initiate and grow. It has been reported that cracks in mechanical joints usually nucleate as corner cracks at the faying surface of joints and grow as elliptical arc through cracks. In this paper, three dimensional finite element analyses are performed for elliptical arc through cracks in mechanical joints. Thereafter stress intensity factors along elliptical crack front including two surface points are determined by the virtual crack closure technique. Virtual crack closure technique is a method to calculate stress intensity factor using the finite element analysis and can be applied to non-orthogonal mesh. As a result, the effects of clearance on the stress intensity factor are investigated and crack shape are then predicted.