Field-programmable gate arrays (FPGAs) based on SRAM cells are an attractive alternative for real-time system designers, as they offer high density, low cost, and high performance. The use of SRAM cells in the FPGA’s configuration memory, while enabling these desirable characteristics, also creates a reliability hazard as RAM cells are susceptible to single-event upsets (SEUs). The usual approach is the use of double or triple redundancy allied with a correction mechanism, such as periodic scrubbing. Although scrubbing is an effective technique to remove SEU-induced errors, the repair of real-time systems presents specific challenges, such as avoiding failures by missing real-time deadlines. In this article, a novel approach is proposed to use a deadline-aware scrubbing scheme with negligible area costs that dynamically chooses the scrubbing starting position. Such a scheme allows us to avoid missing real-time deadlines while maximizing the repair probability given a bounded repair time. Our approach reduces the failure rate, considering the probability of missing deadlines due to faults, by 33.39% on average, with an average area cost of 1.23%.