In this paper, real-time feedback control of a novel micro-machined 1-degree-of-freedom (1-DoF) thermal nanopositioner with on-chip electrothermal positioning sensors is presented. The actuation works based on thermal expansion of silicon beams. The sensing mechanism works based on the difference between the electrical resistances of two electrically biased identical Silicon beams. The difference increases with displacement as the heat conductance of the sensor beams vary oppositely with position, resulting in different beam temperatures and resistances. The sensor pair is operated in a differential way to reduce low-frequency drift. The nanopositioner has a nonlinear static input-output characteristic. An open-loop control system is first designed using polynomials that approximately compensate the nonlinear characteristics. It is experimentally shown that plant uncertainties and sensor drift result in unacceptable performance for open-loop control of the thermal nanopositioner. Hence, feedback control methods are necessary for accurate nanopositioning. A closed-loop feedback control system was then designed using a proportional-integral (PI) controller and the nonlinear compensator used for the open-loop control system. The closed-loop system provides acceptable and robust tracking performance for a wide range of set point values. For triangular reference tracking, which is needed in raster-scanned SPM, the tracking performance of the closed-loop system is further improved by incorporating a suitable pre-filter.