In recent research on building materials, researchers have increasingly focused on replacing cement with agricultural waste. This approach offers significant advantages in terms of reducing global CO2 emissions and promoting the sustainability of building materials. In this paper, the use of the agricultural waste walnut shell ash (WSA) to partially replace cement in sustainable green mortars is explored. Specifically, equal amounts of WSA (5%, 10% and 15%) were used to replace cement. To offset the reduction in strength caused by the partial replacement of cement with WSA, basalt fibers were added to the mortar mixture. The effect of these fibers on the mechanical properties of the WSA-reinforced mortar was examined in compression tests, split tensile tests, and flexural fatigue cycle tests. In the flexural fatigue tests, the parameter and length of basalt fibers were varied and different stress levels (0.85, 0.8 and 0.75) were applied. The fatigue equations were developed using the Weibull model and p–s–n curves with a survival probability of 0.5 were derived. The results showed that the compressive strength and split tensile strength of the specimens increased with the addition of basalt fibers, with maximum values of 34.7 MPa and 3.8 MPa, respectively, and maximum increases of 8.78% and 21.95%, respectively. In addition, the average fatigue life of WSA mortar was 247,541 cycles, which increased by 139.26% when the stress level was 0.75, fiber length was 9 mm, and dosage was 0.3%. The linear regression fitting showed good correlation and provided valuable insights for practical engineering applications.