Few studies have explored the well-being of fathers of children with intellectual disability (ID), despite the significant role that they play in their children's lives. The current study compared fathers of children with and without a child with ID on measures of psychological well-being (life satisfaction, work-family balance and general health) and dimensions of parenting (parenting self-efficacy and parent-child closeness) and then examined whether the presence of a child with ID in the family was a significant predictor of paternal well-being when controlling for a number of father (age, education, employment and residency), child (ID status, gender, behavioural and emotional problems) and family (income poverty and number of children in the household) variables. Data were drawn from the third wave of the Millennium Cohort Study, a UK population-representative and cohort study, where the cohort child was 5 years of age; 256 fathers were identified as having a child with ID, with data available for 10 187 fathers without a child with ID. Fathers were compared on the four well-being and parenting outcomes and then multiple regression models were conducted to explore associations between these outcomes and variables identified as potential correlates of well-being. Initial group comparisons showed that there were differences in the well-being of fathers, with fathers of children with ID reporting poorer life satisfaction and general health. However, these differences were small. Regression analyses showed that child behavioural and emotional problems, living in income poverty and paternal employment were more important than disability status in predicting fathers' well-being. These works add to the limited amount of research on fathers using population-representative data. The current findings are consistent with rejecting a general simplistic and negative narrative that raising a child with ID puts fathers at risk of poorer outcomes. However, some fathers, such as those with children with behavioural problems and living in poverty, may require greater support. Future longitudinal research that explores the impact of paternal well-being on the long-term outcomes of children with and without ID is warranted. © 2019 The Authors. Journal of Intellectual Disability Research published by MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.