Chylothorax occurs in 2.8–5% of infants after cardiac surgery and can increase morbidity and mortality. First-line conservative treatment consists of a chest tube drainage and a fat-free and medium-chain triglyceride (MCT)-enriched diet. This typically leads to a discontinuity of breast milk feeding due to high content of long-chain triglycerides within the breast milk. Modified breast milk with low fat content (LFBM) could provide numerous benefits like immunological properties of breast milk even for patients with chylothorax. This study was conducted at Herzzentrum Leipzig comparing clinical and growth outcomes between infants with chylothorax after surgery for congenital heart disease treated with LFBM (n = 13) versus MCT-Formula (n = 10). LFBM was prepared by centrifugation of native breast milk added with MCT-oil and fortifier. There were no differences in volume and duration of chest tube drainage between LFBM and MCT-formula treatment groups. Furthermore, no statistically significant differences with regard to weight and length gains could be observed between both feeding groups. LFBM is an efficient and unharmful treatment for chylothorax following cardiac surgery in young children.