During long-term service, fatigue cracking usually occurs at the diaphragm arc-shaped cutouts in steel bridges subjected to vehicle-induced vibrations and cyclical wheel loads. To address this issue, the repair methods of bonding carbon fiber reinforced polymer (CFRP) sheets, NiTiNb-based shape memory alloys (NiTiNb-SMA)/CFRP composite patches, and Fe-based shape memory alloys (Fe-SMA) plates were proposed based on the traditional crack-stop hole method. The fatigue performance of 8 repaired diaphragm specimens was examined via experimental research. The fatigue life of the diaphragms repaired by CFRP sheets, NiTiNb-SMA/CFRP composite patches, and Fe-SMA plates are 2.59 times, 5.10 times, and 12.68 times respectively that of the diaphragm repaired solely by crack-stop hole. Based on the China-made Fe-SMA independently developed by the authors, the Fe-SMA plate covering crack-stop hole method was applied to actively repair fatigue cracks at the diaphragm cutouts in Sutong Bridge, detailing the corresponding reinforcement method, construction process, and repair effectiveness. Following reinforcements, compressive stresses of 40–60 MPa were effectively introduced at the edge of the crack-stop hole, which could substantially enhance the anti-fatigue performance of the cracked diaphragms. The feasibility and effectiveness of the Fe-SMA plate covering crack-stop hole method were verified through the practical repair applications of cracked diaphragm cutouts in the Sutong Bridge and some other kilometer-level steel bridges.