Many efforts have been made to understand the mechanism of whiplash injury. Recently, the cervical facet joint capsules have been focused on as a potential site of injury. An experimental approach has been taken to analyze the vertebral motion and to estimate joint capsule stretch that was thought to be a potential cause of pain. The purpose of this study is to analyze the kinematics of the cervical facet joint using a human FE model in order to better understand the injury mechanism. The Total Human Model for Safety (THUMS) was used to visually analyze the local and global kinematics of the spine. Soft tissues in the neck were newly modeled and introduced into THUMS for estimating the loading level in rear impacts. The model was first validated against human test data in the literature by comparing vertebrae motion as well as head and neck responses. Joint capsule strain was estimated from a maximum principal strain output from the elements representing the capsule tissues. A rear-end collision was then simulated using THUMS and a prototype seat model, assuming a delta-V of 25 km/h. The trajectory of the vertebrae was analyzed in a local coordinate system defined along the joint surface. Strain growth in the joint capsules was explained, as related to contact events between the occupant and the seat. A new seat concept was proposed to help lessen the loading level to the neck soft tissues. The foam material of the seat back was softened, the initial gap behind the head was reduced and the head restraint was stiffened for firm support. The lower seat back frame was also reinforced to withstand the impact severity at the given delta-V. Another rear impact simulation was conducted using the new seat concept model to examine the effectiveness of the new concept. The joint capsule strain was found to be relatively lower with the new seat concept. The study also discusses the influence of seat parameters to the vertebral motion and the resultant strain in the joint capsules. The meaning of the contact timing of the head to the head restraint was examined based on the results in terms of correlation with injury indicators such as NIC and the joint capsule strain.