BackgroundInborn errors of amino acid metabolism are chronic conditions that have many sequels. Mothers of these children are facing different challenges which are underdetermined. This study was done to explore lived experience of mothers caring for these children.MethodsThis is an interpretive phenomenology with van Manen’s approach which has 6 steps. Data were gathered by convenience and purposeful sampling. Nine mothers with different experiences were interviewed and the interviews were audiotaped.ResultsSix final themes were revealed from the exploring mothers’ experiences including the future tied to the past, psychosis in the shadow of a lost ideal child, rebellion and blaming, the ways of escaping difficulties, self-forgetting in the shadow of full-time care, passing difficulties in the duality of hope-hopelessness, caring in a continuum of isolation-socialization.ConclusionMothers have multiple challenges in taking care of their children, especially psychologically and financially. So, nurses must plan programs for helping mothers of children with inborn errors of amino acid metabolism to reduce the effects of disease on mothers and consequently the children and the whole family.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-03946-x.