FPGA-based designs are more susceptible to single-event upsets (SEUs) compared to ASIC designs. Soft error rate (SER) estimation is a crucial step in the design of soft error tolerant schemes to balance reliability, performance, and cost of the system. Previous techniques on FPGA SER estimation are based on time-consuming fault injection and simulation methods. In this paper, we present an analytical approach to estimate the failure rate of designs mapped into FPGAs. Experimental results show that this technique is orders of magnitude faster than fault injection method while is very accurate. We also present a high-reliable low-cost mitigation technique which can significantly improve the availability of FPGA-based designs. This technique is able to tolerate SEUs in both user and configuration bits of mapped designs. Categories and Subject Descriptors B.2.3 [Performance and Reliability]: Reliability, Testing, and Fault-Tolerance; B.6.2 [Logic Design]: Reliability and Testing General...