A disorder is considered a rare disease if it affects 1 in 2000, hence, while independently unique, collectively, these conditions are quite common. Many rare diseases are diagnosed during childhood, and therefore parents become primary caregivers in addition to their parental role. Despite the prevalence of rare diseases among children, there has been little research focused on parents' experiences of navigating the healthcare system, a gap we begin to address in this study. Guided by an interpretive description methodology, participants were recruited through online listservs and posting flyers at a pediatric hospital in Western Canada. Sixteen parents (15 mothers and 1 father) participated in in‐depth, semi‐structured interviews between April 2013 and March 2014. Data were analyzed inductively, generating the main study themes. Findings illuminated the challenges parents' experienced on their child's diagnostic journey—from seeking, to receiving, to adjusting to the rare disease diagnosis. Following diagnosis, gaps, and barriers to services resulted in parents pursuing services that could support their child's unique care needs, which often resulted in out‐of‐pocket payments and changes to employment. Parents found peer support, both online and in person, to be an effective resource. This study illustrates the common challenges experienced by parents of children with rare diseases as they navigate the healthcare system. Parents' role as "expert caregiver" was rarely acknowledged by healthcare providers, pointing to the need to foster more egalitarian relationships. As well, parents were burdened with the additional role of care coordinator, a role that could be filled formally by a healthcare provider. Lastly, peer support was a key resource in terms of information and emotional support for parents who often begin their journey feeling isolated and alone. Policies and programs are needed that validate the invisible care work of parents and ensure adequate formal supports are in place to mitigate potential sources of inequity for these families. Furthermore, genetic counselors can play a key role in ensuring parents' informational needs are addressed at the time of diagnosis and in connecting families who share common experiences regardless of the rare disease diagnosis.