This paper presents experimental data from three-point bending fatigue tests of load-carrying cruciform joints with partial penetration fillet welds that are representative of hydraulic turbine runners. The cruciform joints were made by multi-pass FCAW of martensitic stainless steel plates (AISI 415), followed by weld toe grinding and tempering. The S–N approach is used to compare the fatigue performances for three different weld penetration depths covering both weld toe and weld root failures. In case of weld root failure, the variable fatigue lives at the weld roots in a S–N plot are consolidated by introducing an equivalent notch stress intensity factor under mixed-mode. The results demonstrate that the origin of fatigue failure mode transition is size dependent, and it also depends on the nominal stress range and weld toe surface finish. E316L austenitic weld metal yields lower fatigue performance than E410NiMo martensitic weld metal but does not require preheating.