The use of joints fabricated from dissimilar titanium alloys allows the design of structures with local properties tailored to different service requirements. To develop welded structures for aerospace applications, particularly under critical loading, an understanding of the fatigue behavior is crucial, but remains limited, especially for solid-state technologies such as linear friction welding (LFW). This paper presents the fatigue behavior of dissimilar titanium alloys, Ti–6Al–4V (Ti64) and Ti–6Al–2Sn–4Zr–2Mo–0.1Si (Ti6242), joined by LFW with the aim of characterizing the stress versus number of cycles to failure (S-N) curves in both the low- and high-cycle fatigue regimes. Prior to fatigue testing, metallurgical characterization of the dissimilar alloy welds indicated softening in the heat-affected zone due to the retention of metastable β, and the typical practice of stress relief annealing (SRA) for alleviating the residual stresses was effective also in transforming the metastable β to equilibrated levels of α + β phases and recovering the hardness. Thus, the dissimilar alloy joints were fatigue-tested in the SRA (750 °C for 2 h) condition and their low- and high-cycle fatigue behaviors were compared to those of the Ti64 and Ti6242 base metals (BMs). The low-cycle fatigue (LCF) behavior of the dissimilar Ti6242–Ti64 linear friction welds was characterized by relatively high maximum stress values (~ 900 to 1100 MPa) and, in the high-cycle fatigue (HCF) regime, the fatigue limit of 450 MPa at 107 cycles was just slightly higher than that of the Ti6242 BM (434 MPa) and the Ti64 BM (445 MPa). Fatigue failure of the dissimilar titanium alloy welds in the low-cycle and high-cycle regimes occurred, respectively, on the Ti64 and Ti6242 sides, roughly 3 ± 1 mm away from the weld center, and the transitioning was reasoned based on the microstructural characteristics of the BMs.