In this work, we present a compact “adaptive downsampling” method that mitigates the nonlinearity problems associated with FPGA-based TDCs that utilize delay lines. Additionally, this generic method allows for trade-offs between resolution, linearity, and resource utilization. Since nonlinearity is one of the predominant issues regarding delay lines in FPGA-based TDCs, combined with the fact that delay lines are utilized for a wide range of TDC architectures (not limited to the delay-line TDC), other implementations (e.g., Vernier or wave union TDCs), also in different FPGA devices, can directly benefit from the proposed adaptive method, with no need for either custom routing or complex tuning of the converter. Furthermore, implementation-related challenges regarding clock skew, measurement uncertainty, and the placement of the TDC are discussed and we also propose an experimental setup that utilizes only FPGA resources in order to characterize the converter. Although the TDC in this work was implemented in a Xilinx Virtex-6 device and was characterized under different operational modes, we successfully optimized the converter’s nonlinearity and resource utilization while retaining single-shot precision. The best performing (in terms of linearity) implementation reached DNLrms and INLrms values of 0.30 LSB and 0.45 LSB, respectively, and the single-shot precision (σ) was 9.0 ps.