Ferrierite-based catalysts have been evaluated in 1-butene isomerization using a continuous flow reactor operating under microwave and conventional heating conditions. The key feature of this study is the application of a single-mode microwave cavity, which can considerably enhance the heating efficiency compared to traditional microwave ovens. Our results demonstrate that the transformations of low polarity organic compounds over siliceous zeolites can be induced by microwave radiation. Despite the high power density in the utilized single-mode system, no structural degradation of the catalysts has been detected using FTIR and XRD. Our catalytic data confirm that medium-pore ferrierite is an effective isomerization catalyst providing high selectivity towards isobutene, particularly under conditions favoring the monomolecular reaction mechanism. The catalytic performance of ferrierite in the reactions carried out under microwave and conventional heating is very similar, although under the microwave irradiation this zeolite demonstrates a slightly higher yield and selectivity towards isobutene.