With widespread applications in a variety of disciplines, mainly biology and medicine, Polymerase Chain Reaction (PCR) technology has established itself as one of the most significant discoveries of the last 100 years. However, the primary drawback of commercially available PCR instruments is their slow thermal cycling. On the other hand, rapid and efficient microwave (MW) heating offers a viable solution to drastically decrease the time needed for PCR experiments. In this study, we utilize a Complementary Split Ring Resonator (CSRR), operating as a microwave heater at around 3.75 GHz when combined with a microfluidic structure with a 5.4 µl volume. The resulting device exhibits excellent temperature uniformity with high heating and cooling rates of 19°C/s and 18.6°C/s, respectively. Furthermore, model-based frequency-adaptive MW heating was investigated based on optimal heating frequency shift due to the temperature increase of the sample during MW heating, yielding 1.2 W lower applied power and an 8% higher heating efficiency when compared to fixed-frequency heating.