Purpose Due to an increase in survival, a growing population of childhood cancer survivors (CCS) is present. However, female CCS are at risk of developing premature ovarian insufficiency (POI) after cancer treatment. POI involves a decreased chance of conceiving and the increased infertility state has a large impact on affected individuals’ health and mental life. The objective of this study was to investigate health state and well-being among female CCS with and without POI and healthy controls (HC). Methods Female CCS treated in southern Sweden between 1964 and 2008 were included. Each patient was matched with a HC. The final study population included 167 female CCS and 164 HC that were examined between October 2010 and January 2015 at the Reproductive Medicine Centre at Skåne University Hospital in Malmö, Sweden. All participants, except for two HCs, answered an EQ-5D-3L questionnaire for measuring health state including a visual analogue scale (VAS) for estimating well-being. Results There were 22 CCS with POI, none of the HC had POI. The mean health state differed among groups (unadjusted: P = 0.002; adjusted: P = 0.007). A difference in mean experienced well-being among groups was noted (unadjusted: P = 0.003; adjusted: P = 0.012). Lowest well-being was found in the CCS group with POI (P = 0.024). Conclusions Female CCS have a significantly decreased health state and well-being. Female CCS with POI additionally have the lowest self-estimated well-being. Implications for Cancer Survivors Female CCS with POI should be identified early in order to give them adequate information and support.