We evaluated the impact of FLT3 -ITD, NPM1 mutations, and double mutant CEBPa ( dmCEBPa ) on overall survival (OS) after relapse in patients with cytogenetically intermediate-risk acute myeloid leukemia (AML) who were treated with chemotherapy alone in the first remission (CR1). Patients aged 16–65 years diagnosed with cytogenetically intermediate-risk AML, and who achieved CR1 were included. We retrospectively analyzed FLT3 -ITD, NPM1 mutations and CEBPa using samples obtained at diagnosis, which therefore did not affect the therapeutic decisions. Among 235 patients who had achieved CR1, 152 relapsed, and 52% of them achieved second CR. The rate of achieving second CR was significantly higher (85%) in those with dmCEBPa . Patients with FLT3 -ITD had significantly worse OS after relapse than those without (19% vs 41%, p  = 0.002), while OS was comparable between patients with and without NPM1 mutations (37% vs 34%, p  = 0.309). Patients with dm CEBPa had improved OS than those without (61% vs 32%, p  = 0.006). By multivariate analysis, FLT3 -ITD was independently associated with worse OS after relapse hazard ratio (HR) 1.99, 95% CI 1.27–3.12, p  = 0.003, and dmCEBPa with improved OS (HR 0.40, 95% CI 0.17–0.93, p  = 0.033). Our data show that screening for these mutations at diagnosis is useful for facilitating effective therapeutic decision-making even after relapse.