CdTe and CdTe@ZnS quantum dots (QDs) capped with 3-mercaptopropionic acid (MPA), thioglycolic acid (TGA), or glutathione (GSH) have been employed for the first time as luminescent probes for the sensitive and selective detection of peroxynitrite (ONOO⁻) in aqueous solution. The sensitivity of the proposed probe followed the order: MPA–_TGA–CdTe@ZnS>GSH–_TGA–CdTe@ZnS>MPA–CdTe QDs. The varying degree of quenching is elucidated based on the QD–thiolate bond of CdTe@ZnS being more sensitive to oxidation from ONOO⁻ than CdTe. The selectivity of the probe in the presence of co-existing species followed the order: GSH–_TGA–CdTe@ZnS>MPA–_TGA–CdTe@ZnS>MPA–CdTe QDs. QDs capped with MPA showed less selectivity for ONOO⁻ than GSH. The best limit of detection (LOD) of 12.6 nM was obtained for MPA–_TGA–CdTe@ZnS QDs. Time-resolved fluorescence measurements indicated that the interaction between ONOO⁻ and the QDs is static in nature.