A practical and efficient stereoselective synthesis of 3deoxy-D-manno-2-octulosonic acid (Kdo) glycoside was achieved using N-trifluoroacetoimidate as the glycosyl donor with both batch and microfluidic methods. The method used a conformationally constrained glycosyl donor, which has a bulky isopropylidene group at the 4,5-O-position. The strained conformation directed the coordination of the acetonitrile solvent, which led to the enhancement of reactivity and a-selectivity in the glycosylation.