Recently, the catalytic conversion of fructose to 5-hydroxymethylfurfural (5-HMF) has attracted much interest. The idea of a low-cost, sustainable, energy-efficient method is critical to obtain excellent yield and selectivity for the target product 5-HMF. In this work, microwave (MW) irradiation was chosen as a heating source for the conversion of fructose to 5-HMF with the presence of various amorphous carbons containing Brønsted acid sites as catalysts in dimethyl sulfoxide (DMSO) as a solvent. The catalysts’ morphology, surface functional groups, thermal stability, and compositions of the obtained solids were examined by scanning electron microscope (SEM), elemental mapping, thermogravimetric analysis (TGA), Fourier-transform infrared spectroscopy (FT-IR), energy dispersive X-Ray spectroscopy (EDX), Raman spectroscopy and X-ray diffraction (XRD) techniques. The effect of solvent, heating technique, MW power, time, and catalytic loading on the reaction was studied thoroughly. The highest 5-HMF yield of 79.9% and 5-HMF selectivity of 79.7% were achieved with the optimal condition. 5-HMF was easily separated using a liquid-liquid extraction procedure with high purity. Moreover, the catalyst can be quickly recovered and reused. MW irradiation has proved to selectively and efficiently promote the formation of 5-HMF with high yield in a short reaction time. A mechanism for the formation 5-HMF from fructose was also proposed.