The association between healthy eating practices and child dietary intake in childcare centres where parents pack foods from home has received little attention. This study aimed to: (1) Describe the nutritional content of foods and beverages consumed by children in care; and (2) Assess the association between centre healthy eating practices and child intake of fruit and vegetable servings, added sugar(grams), saturated fat(grams) and sodium(milligrams) in care. A cross-sectional study amongst 448 children attending 22 childcare centres in New South Wales, Australia, was conducted. Child dietary intake was measured via weighed lunchbox measurements, photographs and researcher observation, and centre healthy eating practices were assessed via researcher observation of centre nutrition environments. Children attending lunchbox centres consumed, on average 0.80 servings (standard deviation 0.69) of fruit and 0.27 servings (standard deviation 0.51) of vegetables in care. The availability of foods within children’s lunchboxes was associated with intake of such foods (p < 0.01). Centre provision of intentional healthy eating learning experiences (estimate −0.56; p = 0.01) and the use of feeding practices that support children’s healthy eating (estimate −2.02; p = 0.04) were significantly associated with reduced child intake of saturated fat. Interventions to improve child nutrition in centres should focus on a range of healthy eating practices, including the availability of foods packed within lunchboxes.