In this retrospective cohort study, we investigated the impact of tracheostomies on the long‐term survival of children with trisomy 13 syndrome at a Japanese tertiary pediatric center. We compared survival and survival to discharge rates between patients who underwent tracheostomies during their NICU stays (T group, n = 8) and those who did not (non‐T group, n = 11). A total of 19 patients enrolled. Median survival in all patients was 673 (266–1535) days. Significant differences in the 1‐, 2‐, and 3‐year survival rates were found between the T and the non‐T groups (100% vs. 46%, p = 0.018; 88% vs. 18%, p = 0.006; 63% vs. 9%, p = 0.041, respectively). The survival to discharge rate was higher in the T versus non‐T group (75% vs. 45%, p = 0.352). This study highlights a significantly higher long‐term survival of patients with trisomy 13 syndrome who underwent tracheostomies during their NICU stays.