Ninety-seven percent of children who have special health care needs are cared for by their mothers. These mothers cite that their informal care work can be intrinsically rewarding, however, the role is not without substantial difficulties and consequences. We investigated differences in the health and well-being of mothers whose young children do and do not have special health care needs. Quantitative data are drawn from Growing Up in Australia: The Longitudinal Study of Australian Children. This study employs a matched-case control methodology to compare the experiences of a group of 292 mothers whose children are identified as having long term special health care needs to those mothers whose children are typically developing at two time points; Wave 1 (2004) and Wave 3 (2008). The findings support previous research that mothers of children with special health care needs have poorer general health and mental health than mothers whose children do not have special needs. Mothers of children with special health care needs also perceived life as more difficult. Longitudinally, this study also shows that maternal well-being remains relatively stable during the years when children are transitioning to formal schooling. Implications for policy makers, practitioners and early childhood professionals are discussed.