The current study investigated the effect of hot rolling reduction rate of ultra-high strength low alloy steel manufactured via the direct quenching process on microstructure, tensile and high-cycle fatigue properties of the alloy. In order to control the reduction rate of ultra-high strength steels (UHSSs) differently, the steels were produced with two different thicknesses, 6 mm (46.2%—reduction rate, A) and 15 mm (11.5%—reduction rate, B). Then, the two alloys were directly quenched under the same conditions. Both the UHSSs showed martensite in the near surface region and auto-tempered martensite and bainite in the center region. Tensile results showed that alloy A with higher fraction of finer martensite had higher yield strength by about 180 MPa (1523 MPa) than alloy B. The alloy A was also found to possess a higher tensile strength (~2.1 GPa) than alloy B. In addition, alloy A had higher strength than B, and the elongation of A was about 4% higher than that of alloy B. High-cycle fatigue results showed that the fatigue limits of alloys A and B were 1125 MPa and 1025 MPa, respectively. This means that alloy A is excellent not only in strength but also high-cycle fatigue resistance. Based on the above results, the correlation between the microstructure and deformation behaviors were also discussed.