The influence of the functional groups present in the glycosyl donor on the stereoselective glycosylation of 2‐azido‐2‐deoxy sugar thioglycosides under the N‐iodosuccinimide (NIS) and triflic acid (TfOH) mediated glycosylation conditions has been studied in detail. It was observed that beta glycosides of 2‐azido‐2‐deoxy sugar are formed mainly via a stable alpha‐glycosyl triflate intermediate followed by SN2 substitution of the triflate group by the acceptor. The presence of an electron withdrawing functional group such as O‐picoloyl (Pico) in the glycosyl donor facilitates the formation of stable α‐glycosyl triflate to furnish β‐glycosides, whereas the presence of an electron donating hydrogen bond mediating functional group such as p‐methoxybenzyl (PMB) in the glycosyl donor directs the formation of 1,2‐cis glycosides via the glycosyl oxycarbenium ion intermediate with B2,5 and 4H3 conformation. Excellent yields of the β‐glycosides were obtained in case of 2‐azido‐2‐deoxy‐d‐mannose and 2‐azido‐2‐deoxy‐d‐galactose thioglycosides, and 2‐azido‐2‐deoxy‐d‐glucose thioglycosides furnish moderate yields of the β‐glycosides.