18F-FDG PET/CT is rarely used to evaluate extramedullary disease (EMD) in leukemia, and the systemic assessment of non-central nervous system (non-CNS) EMD is unavailable for B-cell acute lymphoblastic leukemia (B-ALL). Here, we assessed EMDs in each patient with relapsed/refractory (r/r) B-ALL, regardless of whether the patient had EMD symptoms. Ninety-one adult patients were included, of them, 48 (52.7%) had undergone allogeneic hematopoietic cell transplantation (allo-HCT), and 17 (18.7%) had accepted chimeric antigen receptor-T (CAR-T) therapy. EMDs were evaluated using PET/CT (n = 50) or CT/MRI/ultrasound (n = 41). The overall incidence of non-CNS EMD was 42.9% (39/91), and PET/CT revealed many more EMD cases (30/50, 60.0%) than other imaging techniques (9/41, 22.0%) (p = 0.0003). Moreover, five patients presenting with MRD positivity harbored concurrent EMDs, as determined by PET/CT. R/R B-ALL patients with non-CNS EMD were reported to have a poor prognosis even after CD19 CAR-T therapy, therefore, we added consolidation treatments to our patients and observed treatment outcomes in the PET/CT group. Twenty-five patients with non-CNS EMD initially received CD19 or CD22 CAR-T cells, and 22 underwent subsequent consolidations, including allo-HCT, reinfusion of CAR-T cells and others. Among 22 patients treated with the combination therapy, overall survival and progression-free survival rates were 89.5% and 69.4% at 12 months, and 70.3% and 45.8% at 24 months, respectively. In conclusion, among heavily treated r/r B-ALL, PET/CT scans identified a higher incidence of non-CNS EMD and hidden EMDs in MRD-positive patients. The treatment strategy of CAR-T followed by consolidation improved the long-term survival of patients with non-CNS EMD.