Transiently-powered devices rely solely on energy harvesters. Such devices typically use capacitors to store the harvested energy, but recent systems employ supercapacitors to store energy for extended operations. In a supercapacitor-based transiently-powered system, the energy-efficient estimation of the state-of-charge (SoC) of a supercapacitor is critical for practical use of the system, due to its tight energy budget. Conventional voltage-based schemes for capacitors do not provide accuracy in SoC estimation for supercapacitors. Also, the supercapacitor-specific SoC estimation which exploits its charge redistribution characteristics provides an accuracy, but the scheme demands significant overhead, and thus, is not applicable to transiently-powered systems, such as wireless sensor nodes. In this article, we specify three requirements for estimating supercapacitor SoC that should be met to function in transiently-powered systems. We then propose a scheme that meets those requirements. The proposed scheme does not require additional hardware, has a low computation cost, and operates when the system is intermittently powered. Thus, the scheme fits the energy-efficient operation of transiently-powered systems. We implemented the proposed scheme in real hardware and evaluated its functionality and accuracy. The proposed scheme estimated the SoC of supercapacitors with high accuracy, in various configurations and use scenarios, while guaranteeing operations in a typical energy harvesting environment.