A novel flow sensor is presented to measure the flow rate within microchannels in a real-time, noncontact and nonintrusive manner. The microfluidic device is made of a fluidic microchannel sealed with a thin polymer layer interfacing the fluidics and microwave electronics. Deformation of the thin circular membrane alters the permittivity and conductivity over the sensitive zone of the microwave resonator device and enables high-resolution detection of flow rate in microfluidic channels using non-contact microwave as a standalone system. The flow sensor has the linear response in the range of 0-150 µl/min for the optimal sensor performance. The highest sensitivity is detected to be 0.5 µl/min for the membrane with the diameter of 3 mm and the thickness of 100 µm. The sensor is reproducible with the error of 0.1% for the flow rate of 10 µl/min. Furthermore, the sensor functioned very stable for 20 hrs performance within the cell culture incubator in 37 °C and 5% CO2 environment for detecting the flow rate of the culture medium. This sensor does not need any contact with the liquid and is highly compatible with several applications in energy and biomedical engineering, and particularly for microfluidic-based lab-on-chips, micro-bioreactors and organ-on-chips platforms.