Myelodysplastic syndrome with isolated del(5q) is a well-recognized entity with a relatively favorable prognosis. Isolated del(5q) in acute myeloid leukemia is rare and acute myeloid leukemia cases with isolated del(5q) are not well characterized. Del(5q) has been shown to be a poor prognostic marker in acute myeloid leukemia based on multivariable analysis in large cohort studies, which contained mostly cases with del(5q) in the context of multiple chromosomal abnormalities. To further characterize acute myeloid leukemia with isolated del(5q), clinicopathologic characterization including mutation analysis was performed. During a 10-year period, we identified 12 cases of acute myeloid leukemia with isolated del(5q), 7 cases of acute myeloid leukemia with del(5q) plus one additional chromosome abnormality not involving chromosome 7, as well as two control groups composed of 124 cases of acute myeloid leukemia with complex karyotype including del(5q), and 40 cases of myelodysplastic syndrome with isolated del(5q). At diagnosis, cases of acute myeloid leukemia with isolated del(5q) had higher platelet counts (p = 0.044), hemoglobin (p = 0.011), and mean corpuscular volume (p = 0.017) compared with cases of acute myeloid leukemia with complex karyotype including del(5q). Acute myeloid leukemia with isolated del(5q) was less likely therapy-related (p = 0.037), more likely to have IDH1/IDH2 mutations (p = 0.009), and less likely to have TP53 mutations (p = 0.005) when compared to acute myeloid leukemia with complex karyotype including del(5q). Acute myeloid leukemia with isolated del(5q) also showed longer overall survival than acute myeloid leukemia with complex karyotype cases including del(5q) (p = 0.004). In summary, acute myeloid leukemia with isolated del(5q) appeared to show some distinct clinicopathologic and genomic features as compared to cases of acute myeloid leukemia with complex karyotype including del(5q).