The development of the Skipper-charge-coupled devices (Skipper-CCDs) has been a major technological breakthrough for sensing very weak ionizing particles. The sensor allows to reach the ultimate sensitivity of silicon material as a charge signal sensor by unambiguous determination of the charge signal collected by each cell or pixel, even for single electron–hole pair ionization. Extensive use of the technology was limited by the lack of specific equipment to operate the sensor at the ultimate performance. A simple, single-board Skipper-CCD controller designed by the authors is presented and aimed for the operation of the detector in high sensitivity scientific applications. Our article describes the main components and functionality of the so-called low threshold acquisition controller together with experimental results when connected to a Skipper-CCD sensor. Measurements show unprecedented deep subelectron noise of 0.039  erms−/pix by nondestructively measuring the charge 5000 times in each pixel.