We present a microfluidic device for specific extraction and thermally activated release of analytes using nucleic acid aptamers. The device primarily consists of a microchamber that is packed with aptamer-functionalized microbeads as a stationary phase, and integrated with a micro heater and temperature sensor. We demonstrate the device operation by performing the extraction of a metabolic analyte, adenosine monophosphate coupled with thiazole orange (TO-AMP), with high selectivity to an RNA aptamer. Controlled release of TO-AMP from the aptamer surface is then conducted at low temperatures using on-chip thermal activation. This allows isocratic analyte elution, which eliminates the use of potentially harsh reagents, and enables efficient regeneration of the aptamer surfaces when device reusability is desired.