This study aimed to evaluate the impact of the myelodysplasia-related gene (MRG) as well as additional gene mutations on outcomes in intensively treated patients with NPM1-mutated (NPM1 ^mut) AML. Targeted DNA sequencing of 263 genes was performed in 568 NPM1 ^mut AML patients (median age: 59 years) entered into the prospective AMLSG 09-09 treatment trial. Most commonly co-mutated genes were DNMT3A (49.8%), FLT3-TKD (25.9%), PTPN11 (24.8%), NRAS (22.7%), TET2 (21.7%), IDH2 (21.3%), IDH1 (18%), and FLT3-ITD (17.3%). MRG mutations were identified in 18.1% of cases (18-60 years: 9.8%; >60 years: 28.7%). When focusing on the 470 patients with 2022 ELN favorable-risk NPM1 ^mut AML, multivariable analysis for event-free survival (EFS) identified age (p < 0.001), DNMT3A ^R882 (p < 0.001), IDH1 (p = 0.007), and MRG mutations (p = 0.03) as unfavorable factors, cohesin gene co-mutations (p = 0.001) and treatment with gemtuzumab ozogamicin (p = 0.007) as favorable factors. Restricting the analysis to a subset of CR/CRi patients with available data on NPM1 ^mut measurable residual disease (MRD) status in blood post cycle 2 in the model, MRG mutations lost their significant effect, whereas DNMT3A ^R882, MYC, and cohesin gene mutations retained the adverse and favorable effects. For OS, age (p < 0.001), DNMT3A ^R882 (p = 0.042), IDH1 (p = 0.045), and KRAS (0.003) mutations were unfavorable factors, sole favorable factor was IDH2 co-mutation (p = 0.037). In 2022 ELN favorable-risk NPM1 ^mut AML, MRG mutations are associated with inferior EFS; however, this effect is no longer present when considering NPM1 ^mut MRD status post cycle 2; DNMT3A ^R882 and MYC mutations remained adverse, and cohesin gene mutations favorable prognostic factors independent of the NPM1 ^mut MRD status.