It is evident that matrix metalloproteinases (MMPs) are involved in the pathophysiology of different inflammatory skin diseases. In this pilot study, we investigated the ability of very high frequency ultrasound—frequencies of approximately 10 MHz—to modulate the activity of MMPs in the skin in inflammatory skin diseases such as acne and rosacea. It was shown that such waves can significantly improve the skin appearance in these diseases; however, the results are dependent on applied treatment schedule. The best results were obtained through the application of a super-fractionation strategy in the form of home treatments carried out twice daily.