Contact Lens-related Discomfort (CLD) is one of the major problems in about 50% of contact lens users. It is a symptom of a variety of conditions such as Lid Wiper Epitheliopathy (LWE), Superior Epithelial Arcuate Lesion (SEAL), Limbal Stem Cell Deficiency (LSCD), Superior Limbic Keratoconjunctivitis (SLK) and dry eye disease; which affect the quality of life. Hence, it is essential to investigate the underlying cause of CLD. During a blink, the under surface of the eyelid tends to interact with the cornea and the conjunctiva. The presence of a contact lens can add to the biomechanical changes on these surfaces. To estimate these changes with and without a contact lens, a Finite Element Model (FEM) of the eyelid wiper, eyeball and contact lens was developed using COMSOL Multiphysics®. Biomechanical properties such as von Mises stress and displacement were calculated. Our study concluded that large stress formed in the lid wiper could be the reason for the occurrence of LWE and SLK without contact lens in the eye. When the contact lens was in situ, large stress was found in the superior 1.3mm of the cornea which could be responsible for the development of SEAL and superior LSCD.