Most per- and poly-fluoroalkyl substances (PFAS) lack toxicity data, and the hazards associated with different PFAS chemical structures have not been systematically assessed using in vivo models. To address this gap, we compared the toxicity of nine PFAS in embryo-larval zebrafish, an emerging alternative to conventional in vivo models. Exposures were conducted from 0 to 5 days post-fertilization with semi-static renewal. We then evaluated three apical toxicity endpoints (developmental toxicity (mortality/malformation), swimming behaviour, and metabolic activity) alongside gene expression changes using high-throughput transcriptomics. These data were used to derive apical and transcriptomic points of departure (aPODs and tPODs, respectively). Transcriptomic benchmark concentration modeling in BMDExpress v3.2 was performed to derive tPODs using multiple approaches. Overall, PFAS potency increased with longer fluorinated carbon chain lengths and was greater for PFAS containing sulfonic groups. tPODs were generally the most sensitive endpoints, typically falling within a 10-fold range below aPODs. Our results support previous findings that tPODs provide suitably conservative PODs for chemical toxicity assessment. Our results contribute new data on PFAS early-life stage toxicity and demonstrate an economical and ethically viable high-throughput platform for systematic evaluation of chemical hazards and potencies for risk assessment applications.