Background and objective: Perfluoroalkyl substances (PFASs), including perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), perfluorohexane sulfonic acid (PFHxS), and perfluorononanoic acid (PFNA), have been associated with adverse bone, and metabolic changes in adults. However association of PFASs with bone health in children is understudied. Considering their role as endocrine disruptors, we examined relationships of four PFASs with bone health in children. Methods: In a cross sectional pilot study, 48 obese children aged 8–12 years were enrolled from Dayton's Children Hospital, Ohio. Anthropometric, clinical and biochemical assessments of serum were completed. Serum PFASs were measured by UPLC-ESI-MS/MS. In a subset of 23 children, bone health parameters were measured using calcaneal quantitative ultrasound (QUS). Results: While PFASs exposure was associated with a consistent negative relationship with bone health parameters, among four PFASs tested, only PFNA showed a significant negative relationship with bone parameter (β [95% CI], = − 72.7 [− 126.0, − 19.6], p =.010). PFNA was also associated with raised systolic blood pressure (p =.008), low density lipoprotein cholesterol (LDL-C; p <.001), and total cholesterol (TC; p =.014). In addition, both PFOA and PFOS predicted elevation in LDL-C, and PFOA predicted increased TC, as well. In this analysis, PFASs were not strongly related to thyroid hormones, 25-hydroxy vitamin D, liver enzymes, or glucose homeostasis. Conclusion: PFASs exposure in obese children may play a role in adverse skeletal and cardiovascular risk profiles.