In this study, we propose a robust field-programmable gate array (FPGA)-based time-to-digital converter (TDC) with run-time calibration. A code density test was used for differential nonlinearity (DNL) calibration to deal with nonuniformity in delay cells. The proposed calibration scheme is implemented as a four-step finite state machine (FSM) for run-time calibration. We implemented the TDC with the proposed run-time calibration circuit on the Xilinx 65-nm FPGA platform. This improved the DNL and integral nonlinearity (INL) values over those obtained using a TDC without run-time calibration circuit. The DNL and INL values at a time resolution of 46.875 picoseconds were [−0.68, 1.04] and [−4.27, 2.27] least significant bits, respectively. More than 30% DNL and INL improvements are achieved for the TDC with calibration circuit. The results obtained at temperatures of 27 • C to approximately 70 • C indicated that the proposed run-time calibration circuit enhanced the capability of the FPGA-based TDC against temperature effects. The FPGA-based TDC with the proposed run-time calibration FSM provides robust high-resolution performance suited for a range of scientific applications. KEYWORDS differential nonlinearity (DNL), field-programmable gate array (FPGA), run-time calibration, time-to-digital converter (TDC) Int J Circ Theor Appl. 2019;47:19-31.wileyonlinelibrary.com/journal/cta