In this paper, we are concerned about the problem of guaranteeing both privacy and security in a Location-Based Service (LBS) system, where a challenging scenario involving cooperative attack is considered. Since prior Physical-Layer Authentication (PLA) schemes do not consider cooperative attack, their security significantly declines under such attacks. We propose two privacy-preserving PLA schemes: the Privacy-Preserving Physical-Layer Authentication using Noise Variance (PPPLA-NV) scheme and the Privacy-Preserving Physical-Layer Authentication using Multiple Channel Responses (PPPLA-MCR) scheme, which significantly improve the privacy-preserving performance under a cooperative attack. Note that the proposed schemes protect not only user’s identity information but also data message. We theoretically analyze the performance of the proposed schemes, derive their closed-form expressions, and provide a theoretical comparison between both proposed schemes. We implement the proposed schemes and conduct extensive performance comparisons through simulations. Experimental results show a perfect match between the theoretical and simulation results. From the experimental results, we observe that if the overhead is not the priority, the PPPLA-MCR scheme is the best option; otherwise, the PPPLA-NV scheme may be a better option.