Purpose In two-stage prosthetic breast reconstruction, autologous fat graft (AFG) is often conducted simultaneously with the second-stage operation, which is usually performed shortly after mastectomy. There is a paucity of studies evaluating whether conducting AFG early, with a relatively short interval from the primary operation, is oncologically safe. This study aimed to evaluate potential associations of AFG with breast cancer prognosis, focusing on its timing. Methods Patients with invasive breast cancer who underwent immediate two-stage prosthetic reconstruction following mastectomy between 2011 and 2016 were identified. They were categorized into two groups by whether AFG was performed during the second-stage operation. Cumulative incidence of oncologic events was compared between the two groups, after stratifying patients by the time interval between mastectomy and the second-stage operation (≤ 12 months vs. > 12 months). Results Of 267 cases that met the selection criteria, 203 underwent the second-stage operation within 12 months of mastectomy. AFG was performed for 112 cases and was not performed in 91 cases. The two groups showed similar baseline characteristics including tumor stage and adjuvant treatments. Compared with the control, AFG was associated with lower locoregional recurrence-free survival and disease-free survival, and this difference remained significant after adjusting for other variables including tumor stage. In the 64 cases undergoing the operation after 12 months following mastectomy, oncologic outcomes did not differ between the two groups. Conclusion Our results suggest that AFG timing in relation to mastectomy may be associated with risks for breast cancer recurrence.