Introduction This study explored the effects of prenatal exposure to fumonisins B (FB) on bone innervation in newborn Wistar rats. Material and Methods Pregnant dams (n = 6 per group) were assigned to either the control or one of two FB-exposed groups (60 mg or 90 mg/kg body weight) from the 7th day of gestation until parturition. On the day of parturition, one male pup from each litter (n = 6 per group) was randomly selected and euthanised, and their femurs were dissected for analysis. Bone innervation was quantified by examining the morphology patterns of sympathetic, parasympathetic, sensory and cocaine- and amphetamine-regulated transcript (CART)-positive fibres. Prepared bone sections were analysed using immunohistochemistry staining for protein gene product 9.5, tyrosine hydroxylase, choline acetyltransferase, vasoactive intestinal peptide (VIP), substance P and CART-positive neurons. Results The group that received a higher dose of FB demonstrated an increase in both the size and complexity of the complete bone neuronal network together with heightened sympathetic and sensory innervation, and displayed a decrease in neuron density and sympathetic innervation. Fumonisin B exposure led to a decrease in galanin-positive and VIP-positive bone neuronal networks in both groups exposed to FB, while in the lower-dose group, there was also a decrease in CART-positive innervation. Conclusion Prenatal FB exposure significantly influences the neuronal bone network of rats, which is essential for maintaining bone homeostasis. These findings emphasise the necessity for further research to understand the lasting effects and underlying mechanisms of alterations induced by FB.