This paper proposes a method for process parameter optimization of a mobile robotic percussive riveting system with flexible joints to guarantee the rivet gun alignment during the operation. This development is motivated by the increasing interest in using industrial robots to replace human operators for percussive impact riveting in aerospace assembly. In percussive riveting, the rivet gun generates repetitive impacts acting on the rivet. These impacts not only deform the rivet but also induce forced vibration to the robot, and thus the robot must hold the gun firmly during riveting. The process parameters for the mobile robotic riveting system include those related to the impact force generation for planning the rivet gun input and those related to the robot pose with respect to the joined panels for planning the mobile platform motion. These parameters are incorporated into a structural dynamic model of the robot under a periodic impact force. Then an approximate analytical solution is formulated to calculate the displacement of the rivet gun mounted on the end-effector for its misalignment evaluation. It is found that both the force frequency and the mobile platform position have strong influence on the robotic riveting performance in terms of alignment during operation. Global optimization of these process parameters is carried out to demonstrate the practical application of the proposed method for the planning of the robotic percussive riveting system.