Background/Objectives: Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent chemicals widely detected in aquatic systems and drinking water. Perfluorononanoic acid (PFNA), a long-chain PFAS, has been reported globally in environmental matrices and fish tissues. Although PFNA has been linked to developmental, metabolic, and neurological toxicity, its effects on lipid-related pathways and neurotoxicity remain poorly characterized. Methods: This study evaluated the developmental and neurotoxic effects of PFNA exposure in zebrafish embryos and larvae following a 7-day exposure to environmentally relevant PFNA concentrations. Results: PFNA exposure did not significantly affect survival or deformity rates at the concentrations tested. Apoptosis was significantly increased in larvae exposed to 1 µg/L PFNA compared to controls, whereas reactive oxygen species levels were unaffected. Two concentrations (0.1 µg/L and 10 µg/L) were further examined for transcriptomic responses, and the transcriptome response was largely different for each concentration. Low-dose PFNA exposure primarily affected lipid transport, cholesterol metabolism, sphingolipid signaling, and neurodegeneration-related pathways, whereas high-dose PFNA altered transcripts related to synaptic signaling, axon guidance, and thyroid hormone synthesis. Hypoactivity was observed in the movement of larval zebrafish based on a Visual Motor Response test. Conclusions: Taken together, PFNA exposure induced molecular changes related to neurotoxicity and lipid metabolism in zebrafish, which may contribute to adverse neurodevelopmental outcomes.