Objective A robotic navigation system for cannulated screw fixation of femoral neck fracture has been developed and applied in clinical trials. A data envelopment analysis (DEA) based method has been proposed and implemented to evaluate the efficiency of this system. It can provide a support for the clinical efficiency in the quantitative evaluation of the robotic navigation system. Methods The robotic navigation system used bi-planar algorithm to calculate the spatial position and orientation of the operation path from two intra-operative fluoroscopy images. The system also used a novel serial-parallel structured robot to navigate the surgeons to operate following the calculated operation path. Femoral neck surgeries with and without the robotic system were modeled as DMUs. Totally 25 clinical trials which had been done with the assistance of the robotic navigation system were chosen as experiment group, and another 25 cases which had been done in traditional ways were chosen as control group. C2R model was chosen to calculate the DEA efficiency. Efficiency index V in dual program model was used as the criteria to judge whether the DMU was DEA efficient. If V=1, the DMU was DEA efficient, if V<1, the DMU was non-DEA efficient. Results The efficiency index of robot assisted surgery was 1, and the efficiency index of traditional surgery was 0.9863388. According to the definition of DEA model, this result proved the high efficiency of the robotic system. Conclusions The DEA-based evaluation proved that this robotic navigation system could indeed improve clinical efficiency.