Sialin, encoded by the <i>SLC17A5</i> gene, is a lysosomal sialic acid transporter defective in Salla disease, a rare inherited leukodystrophy. It also enables metabolic incorporation of exogenous sialic acids, leading to autoantibodies against <i>N</i>-glycolylneuraminic acid in humans. Here, we identified a novel class of human sialin ligands by virtual screening and structure-activity relationship studies. The ligand scaffold is characterized by an amino acid backbone with a free carboxylate, an <i>N</i>-linked aromatic or heteroaromatic substituent, and a hydrophobic side chain. The most potent compound, <b>45</b> (LSP12-3129), inhibited <i>N</i>-acetylneuraminic acid <b>1</b> (Neu5Ac) transport in a non-competitive manner with IC<sub>50</sub> ≈ 2.5 μM, a value 400-fold lower than the <i>K</i><sub>M</sub> for Neu5Ac. In vitro and molecular docking studies attributed the non-competitive character to selective inhibitor binding to the Neu5Ac site in a cytosol-facing conformation. Moreover, compound <b>45</b> rescued the trafficking defect of the pathogenic mutant (R39C) causing Salla disease. This new class of cell-permeant inhibitors provides tools to investigate the physiological roles of sialin and help develop pharmacological chaperones for Salla disease.