Background: Changes in body composition may be used for monitoring progression/ regression of a disease. Prompt γ-rays in vivo neutron activation analysis (IVNAA) has been widely used for the measurement of body composition in recent years.Objective: In this paper, we tried to improve the safety of IVNAA operator.Methods: The most important factor for reducing the operator receiving dose is the optimization of shields. An appropriate shield should not only reduce the operator receiving dose, but it also must have the least effect on the detected spectrum. Because all parts of setup, including the operator shield, can be activated, the emitted γ-rays may be counted in detectors and increase the background level. In this research, several shields have been considered for an IVNAA setup. 4 different shields—concrete, epoxy colemanite resin, paraffin borated with bismuth layer (PE-Bi layer), and paraffin borated uniformly mixed with bismuth (PE-Bi)—were simulated by MCNPX code.Results: We found that the PE-Bi shield decreases the absorbed dose to 77% compared with “no shield” and 74% compared to concrete. Also, the reduction rate of dose equivalent was 95% compared to “no shield” and 91% compared to colemanite resin. The neutron flux decreased almost 400 times in the presence of PE-Bi; it had less background in γ-spectrum compared to other suggested shields.Conclusion: Among the tested shields, PE-Bi would be the best one.