Catalytic dehydration of fructose into 5-hydroxymethylfurfural by microwave heating was studied in acetone-water mixtures in the presence of a cation exchange resin catalyst. The use of acetone–water reaction media resulted in yields of 5-HMF as high as 73.4% for 94% conversion at 150 °C. It was confirmed that there was no decrease of catalytic activity and selectivity for five reuses of the resin, which was in accordance with the elemental analysis results that showed that sulfonic acid groups attached on the resin were stable at the experimental conditions. A comparison between conventional sand bath heating and microwave heating revealed that the latter had a remarkable accelerating effect not only on fructose conversion, but also on 5-HMF yield. Under the conditions (5 ml of 2 wt% fructose solution, 0.1 g of resin, 150 °C and 10 min), fructose conversion and HMF yields by microwave heating (91.7% and 70.3%, respectively) were higher than those by sand bath heating (22.1% and 13.9% respectively). Therefore, the process that we developed in this study showed that high 5-HMF yields from fructose could be achieved under mild conditions.