Treating carbapenem-resistant Klebsiella pneumoniae (CRKP) is challenging, particularly when resistance is mediated by New Delhi metallo-β-lactamase (NDM). Clinical experience with fixed-combination aztreonam–avibactam (ATM–AVI) in young infants remains extremely limited. Here, we report a case of a 2-month-old boy who underwent emergency laparotomy for intestinal obstruction owing to small bowel volvulus with segmental necrosis, followed by bowel resection and reanastomosis. His postoperative course was complicated by respiratory failure, coagulopathy, septic shock, recurrent abdominal distension, and massive ascites. Blood cultures were negative, whereas metagenomic next-generation sequencing of blood detected K. pneumoniae and Enterococcus faecium. Owing to the worsening of his condition, diagnostic paracentesis and repeat laparotomy were performed, revealing an anastomotic leak. Intraoperative pus culture yielded blaNDM-positive CRKP. The isolate was resistant to carbapenems and ceftazidime–AVI but was susceptible to ATM–AVI, with a minimum inhibitory concentration of ≤4 mg/L. ATM–AVI was administered at 30 mg/kg every 8 h, based on the aztreonam component, for 14 days; linezolid and fluconazole were co-administered as part of the broader anti-infective regimen. The combination of definitive surgical source control, targeted antimicrobial therapy, and comprehensive intensive care successfully controlled the infection and stabilized his hemodynamics. The patient defervesced within 24 h of the first ATM–AVI dose. Inflammatory markers declined rapidly, allowing safe extubation. Follow-up abdominal cultures remained negative. No hepatic or renal toxicity was observed during treatment. This case suggests that, when combined with adequate surgical source control, ATM–AVI may represent a valuable mechanism- and susceptibility-guided pharmacological component in a multidisciplinary treatment paradigm for severe blaNDM-positive CRKP infections in selected infants.