High quality care in pediatrics involves shared decision making (SDM) between families and providers. The extent to which children with common mental health disorders experience SDM is not well known. The objectives of this study were to examine how parent-reported SDM varies by child health (physical illness, mental health condition, and comorbid mental and physical conditions) and to examine whether medical home care attenuates any differences. We analyzed data on children (2-17 years) collected through the 2009/2010 National Survey of Children with Special Health Care Needs. The sample consisted of parents of children in one of three child health categories: (1) children with a chronic physical illness but no mental health condition; (2) children with a common mental health condition but no chronic physical condition; and (3) children with comorbid mental and chronic physical conditions. The primary dependent variable was parent-report of provider SDM. The primary independent variable was health condition category. Multivariate linear regression analyses were conducted. Multivariate analyses controlling for sociodemographic variables and parent-reported health condition impact indicated lower SDM among children with a common mental health condition-only (B = -0.40; p < 0.01) and children with comorbid conditions (B = -0.67; p < 0.01) compared to children with a physical condition-only. Differences in SDM for children with a common mental health condition-only were no longer significant in the model adjusting for medical home care. However, differences in SDM for children with comorbid conditions persisted after adjusting for medical home care. Increasing medical home care may help mitigate differences in SDM for children with mental health conditions-only. Other interventions may be needed to improve SDM among children with comorbid mental and physical conditions.