Copper indium sulfide (CIS) quantum dots (QDs) are attractive as labels for biomedical imaging, since they have large absorption coefficients across a broad spectral range, size- and composition-tunable photoluminescence from the visible to the near-infrared, and low toxicity. However, the application of NIR-emitting CIS QDs is still hindered by large size and shape dispersions and low photoluminescence quantum yields (PLQYs). In this work, we develop an efficient pathway to synthesize highly luminescent NIR-emitting wurtzite CIS/ZnS QDs, starting from template Cu2-x S nanocrystals (NCs), which are converted by topotactic partial Cu+ for In3+ exchange into CIS NCs. These NCs are subsequently used as cores for the overgrowth of ZnS shells (≤1 nm thick). The CIS/ZnS core/shell QDs exhibit PL tunability from the first to the second NIR window (750-1100 nm), with PLQYs ranging from 75% (at 820 nm) to 25% (at 1050 nm), and can be readily transferred to water upon exchange of the native ligands for mercaptoundecanoic acid. The resulting water-dispersible CIS/ZnS QDs possess good colloidal stability over at least 6 months and PLQYs ranging from 39% (at 820 nm) to 6% (at 1050 nm). These PLQYs are superior to those of commonly available water-soluble NIR-fluorophores (dyes and QDs), making the hydrophilic CIS/ZnS QDs developed in this work promising candidates for further application as NIR emitters in bioimaging. The hydrophobic CIS/ZnS QDs obtained immediately after the ZnS shelling are also attractive as fluorophores in luminescent solar concentrators.