Survivors of childhood acute lymphoblastic leukemia (cALL) are at high risk of developing dyslipidemia, including low HDL-cholesterol (HDL-C). This study aimed to examine the associations between food/nutrient intake and the levels of HDL-C in a cohort of children and young adult survivors of cALL. Eligible participants (n = 241) were survivors of cALL (49.4% boys; median age: 21.7 years old) recruited as part of the PETALE study. Nutritional data were collected using a validated food frequency questionnaire. Fasting blood was used to determine participants’ lipid profile. Multivariable logistic regression models were fitted to evaluate the associations between intakes of macro- and micronutrients and food groups and plasma lipids. We found that 41.3% of cALL survivors had at least one abnormal lipid value. Specifically, 12.2% had high triglycerides, 17.4% high LDL-cholesterol, and 23.1% low HDL-C. Low HDL-C was inversely associated with high intake (third vs. first tertile) of several nutrients: proteins (OR: 0.27, 95% CI: 0.08–0.92), zinc (OR: 0.26, 95% CI: 0.08–0.84), copper (OR: 0.34, 95% CI: 0.12–0.99), selenium (OR: 0.17, 95% CI: 0.05–0.59), niacin (OR: 0.25, 95% CI: 0.08–0.84), riboflavin (OR: 0.31, 95% CI: 0.12–0.76) and vitamin B12 (OR: 0.35, 95% CI: 0.13–0.90). High meat consumption was also inversely associated (OR: 0.28, 95% CI: 0.09–0.83) with low HDL-C while fast food was positively associated (OR: 2.41, 95% CI: 1.03–5.63) with low HDL-C. The role of nutrition in the development of dyslipidemia after cancer treatment needs further investigation.