Childhood obesity is increasing in Sweden. All children are offered regularly spread health visits to a school nurse. As health visits include a measure of height and weight and a health dialogue, school nurses can discover, disclose, and treat a child's weight gain. The aim of this study was to describe school nurses’ experiences and challenges in working with childhood obesity. This qualitative study collected data through focus-group discussion and semi-structured interviews with ten female school nurses from six municipalities. Data were analysed inductively using manifest qualitative content analysis. The study was reported using the COREQ guidelines. Stigmatization and lack of resources are major challenges for school nurses working with childhood obesity, and they experience frustration, powerlessness and feel that they provide unequal treatment. The present study concludes that obesity stigmatization is a widespread challenge for school nurses. They cannot alone generate all the resources needed or conquer all challenges. Evidence-based guidelines, increased knowledge, time for reflections and peer support could potentially empower school nurses, reduce frustration, and improve the quality of and equality in childhood obesity treatment.