Female incarceration is rising steeply in Australia and other high-income countries. The majority of incarcerated women are mothers. Their children represent a particularly vulnerable group, often subject to adverse experiences due to their family’s disadvantaged circumstances involving inadequate housing, food insecurity, poverty, poor health, a lack of personal safety due to violence and resulting trauma. This qualitative study explores parenting experiences of incarcerated mothers separated from their children. Interviews involved 65 mothers in three Australian prisons and 19 stakeholders providing correctional services and support for incarcerated women. Data were analysed using interpretive description. Mothers’ accounts highlighted frustrations resulting from trying to maintain relationships with their children, often exacerbating their separation and compounding parenting difficulties. Two major themes emerged from the data: ‘protecting their children’ and ‘at the mercy of the system’. Mothers described how they tried to protect their children from the consequences of their incarceration, yet many of the correctional system processes and procedures made it even harder to maintain connection. Incarcerated mothers need support in their parenting role. Ideally, this support should commence during incarceration. Further, changes within prison routines could enhance mothers’ efforts to keep in contact with their children, through visits and phone calls.