Pediatric AML with NUP98-NSD1 fusion defines a high-risk subset with a low remission and high relapse rates. There are a few studies on successful treatment of high-risk AML expressing NUP98-NSD1. We report a refractory pediatric case who received successful treatment with Bcl-2 inhibitor, venetoclax plus DCAG chemotherapy followed by HSCT, after two failure courses of conventional chemotherapies. Our case suggests that the combination of venetoclax and DCAG chemotherapy may be an effective salvage strategy to refractory AML with NUP98-NSD1. More studies and clinical trials should focus on the synergistic effect of Bcl-2 inhibitors and hypomethylation agents, especially in pediatric AML.