School environments can create healthy settings to foster children’s health and well-being. School gardening is gaining popularity as an intervention for healthier eating and increased physical activity. We used a systematic realist approach to investigate how school gardens improve health and well-being outcomes for school-aged children, why, and in what circumstances. The context and mechanisms of the specific school gardening interventions (n = 24) leading to positive health and well-being outcomes for school-aged children were assessed. The impetus of many interventions was to increase fruit and vegetable intake and address the prevention of childhood obesity. Most interventions were conducted at primary schools with participating children in Grades 2 through 6. Types of positive outcomes included increased fruit and vegetable consumption, dietary fiber and vitamins A and C, improved body mass index, and improved well-being of children. Key mechanisms included embedding nutrition-based and garden-based education in the curriculum; experiential learning opportunities; family engagement and participation; authority figure engagement; cultural context; use of multi-prong approaches; and reinforcement of activities during implementation. This review shows that a combination of mechanisms works mutually through school gardening programs leading to improved health and well-being outcomes for school-aged children.