Time-to-digital converters are a key component in many photonics systems, ranging from LiDAR, quantum key distribution, quantum optics experiments and time correlated single photon counting applications. A novel efficient timeto- digital converter non-linearity calibration technique has been developed and demonstrated on a Spartan 6 LX150 field programmable gate array (FPGA). Most FPGA based time-to-digital converters either use post processing or have calibration techniques which do not focus on minimizing resource utilization. With the move towards imaging with arrays of single photon detectors, scalable timing instrumentation is required. The calibration system demonstrated minimizes block memory utilization, using the same memory for probability density function measurement and cumulative distribution function generation, creating a look up table which can be used to calibrate the sub-clock timing module of the time-to-digital converter. The system developed contains 16 time-to-digital converters and demonstrates an average accuracy of 21ps RMS (14.85ps single channel) with a resolution of 1.86ps.