Haploidentical stem cell transplantation (haplo-HSCT) with post-transplant cyclophosphamide (PTCy) is a therapeutic option for secondary acute myeloid leukemia (sAML). The study aimed to compare peripheral blood stem cells (PBSC) vs. bone marrow (BM) as a graft source for haplo-HSCT with PTCy in patients with sAML in first complete remission. A total of 554 patients were included, BM = 136, PBSC = 418. Median follow-up was 3 years. The median year of transplant was 2018 (range, 2010–2021). The antecedent hematological disease was myelodysplastic syndrome /myeloproliferative neoplasms in most patients. Patients in the BM group were younger, median age 59.2 vs. 61.7 years (p = 0.008), and received myeloablative conditioning more frequently (66.4% vs. 47.4%, p < 0.001). Time from diagnosis to haplo-HSCT was 5.3 vs. 4.8 months, respectively (p = 0.019). Performance status, cytogenetic risk, gender, cytomegalovirus serostatus, and donor age did not differ. There were no differences between the groups with respect to main transplantation outcomes. In conclusion, outcomes of haplo-HSCT with PTCy in sAML with either PBSC or BM grafts are similar, with no differences in major transplantation outcomes.