Manipulator joint clearance is a natural consequence of manufacturing processes. Although most studies in the literature have assumed zero joint clearance, its existence is unavoidable and thus its impact needs to be evaluated. With the miniaturizing trend in engineering products, errors due to joint clearance have become an increasingly important issue. This study investigates how manipulators deviate from the desired working sites due to joint clearance. Deviations from the target locations can be reduced by properly selecting the working path. The optimal path is obtained by first parameterizing the path based on the required target task locations. Corresponding controlling inputs, namely linear and angular velocities as well as their accelerations, are calculated using inverse kinematics. Joint clearances are then added to obtain the deviations a path will make. An optimization framework with path parameters as the design variables is then formulated to minimize the resulting deviations. The proposed framework is shown to improve accuracy without additional equipment cost or control effort. A five-bar parallel manipulator is used to demonstrate the proposed method.