Chiral drugs play an essential role in medical and biochemical systems, and thus enantioselective analysis of chiral molecules has become a central focus in chemical, biological, medical, and pharmaceutical research. The design of chiral drug-detecting systems is a long-term and challenging task. Here we report the use of a modification-free nanochannel method for enantioselective recognition of S-naproxen from R-naproxen using N-acetyl-l-cysteine-capped gold nanoparticles as a chiral selector. The chiral discrimination is based on a drug-induced nanoparticle diastereoselective aggregation mechanism that blocks ion transport through the nanochannel. We demonstrated that high S-Npx selectivity in both water and biological samples can be achieved. This simple method has potential applications as a general platform for the detection of chiral molecules.