This thesis proposes optimisation methods for improving the timing performance of digital circuits implemented in Field-Programmable Gate Arrays (FPGAs) with the knowledge of process variation. With the current trend of transistor scaling, improvements in fabrication processes alone will not completely solve the problem of process variability due to the physical limitation of the process and materials. Therefore, higher-level optimisation strategies, such as variation-aware and adaptive design are required to alleviate the erosion of overall timing performance. Three novel optimisation methods, including variation-aware placement, routing and retiming are introduced in this thesis to reduce the impact of process variation on FPGAs us...