BACKGROUNDFlow chemistry is becoming an essential technique in organic synthesis. This trend is expected to continue and broaden in scope and complexity. This miniaturized protocol that includes microreactors enables excellent heat transfer, low solvent wastage, shorter reaction times, higher productivity, and higher space‐time yields.RESULTSIn this study, we synthesized four ionic liquids and applied them as catalysts for the selective preparation of 5‐HMF from fructose using the continuous flow system. The effects of reaction time and temperature, catalyst loading, solvent, and substrates for carbohydrate conversion to 5‐HMF have been carefully investigated, and 5‐HMF yields were determined by the HPLC method.CONCLUSIONSAs a result, 1‐(4‐sulfobutyl)pyridinium iron (III) chloride gave 71% yield of 5‐HMF for 30 min. The results of this research demonstrate that this approach is not only straightforward in design but also rapid and convenient in operation, and it has the potential to be carried out on a massive scale.This article is protected by copyright. All rights reserved.