We report herein the successful preparation of a compact and functional CdSe–ZnS core–shell quantum dot (QD)–DNA conjugate via highly efficient copper-free “click chemistry” (CFCC) between a dihydro-lipoic acid–polyethylene glycol–azide (DHLA–PEG–N3) capped QD and a cyclooctyne modified DNA. This represents an excellent balance between the requirements of high sensitivity, robustness and specificity for the QD-FRET (Förster resonance energy transfer) based sensor as confirmed by a detailed FRET analysis on the QD–DNA conjugate, yielding a relatively short donor–acceptor distance of ∼5.8 nm. We show that this CFCC clicked QD–DNA conjugate is not only able to retain the native fluorescence quantum yield (QY) of the parent DHLA–PEG–N3 capped QD, but also well-suited for robust and specific biosensing; it can directly quantitate, at the pM level, both labelled and unlabelled complementary DNA probes with a good SNP (single-nucleotide polymorphism) discrimination ability in complex media, e.g. 10% human serum via target-binding induced FRET changes between the QD donor and the dye acceptor. Furthermore, this sensor has also been successfully exploited for the detection, at the pM level, of a specific protein target (thrombin) via the encoded anti-thrombin aptamer sequence in the QD–DNA conjugate.