Abstract Aims Having a child with congenital heart disease (CHD) can affect parental health-related quality of life (HR-QoL). We investigated the long-term trajectories of mental HRQoL (m-HRQoL) in mothers of children with CHD and examined risk factors for persistent low m-HRQoL. Methods One hundred twenty-five mothers of children with CHD completed a standardized questionnaire on m-HRQoL (mental subscale SF-12) after the children’s first open-heart surgery and subsequently when the children were 1, 4, 6, 10, and 13 years old. A z-score for m-HRQoL was calculated with national norms. Latent class growth analysis (LCGA) was used to identify subgroups of mothers with regards to their m-HRQoL trajectories over time. Regression analysis investigated predictors for chronically low m-HRQoL. Results Compared to norms, mothers of children with CHD had significantly lower m-HRQoL immediately after open-heart surgery (β = −0.30 (CI-95: −0.44, −0.15)). Subsequently, m-HRQoL increased to a normal level (m-HRQoL compared to the norm from 1 to 13 years: β ranges between 0.05 and 0.27). LCGA revealed two distinct groups of m-HRQoL trajectories: A group with normal m-HRQoL (75% of mothers, means z-scores range between − 0.76 and 0.62) and a group with chronically low m-HRQoL (25% of mothers, mean z-scores range between −1.32 and −0.10). Chronically, low m-HRQoL was associated with poorer social support (OR = 3.39 (CI-95: 1.40, 8.49), p = 0.008) but not with parental education, migration background, number of open-heart surgeries, diagnosis of a univentricular CHD, or low IQ. Conclusion A quarter of mothers of children with CHD have chronically low m-HRQoL throughout their child’s development, especially those mothers with poor social support. Further studies of family-oriented approaches are needed to identify and support these mothers and reinforce parental well-being.