Background The most abundant polychlorinated biphenyl (PCB) congeners found in the environment and in humans are the ortho-substituted, non-dioxin-like (NDL) congeners, especially PCB153. While evidence indicates that exposure to PCB153 and other NDL-PCBs in early vertebrate development can contribute to neurobehavioral disorders, the basis of neurobiological effects of NDL-PCBs is poorly understood. Methods We assessed a range of effects of several NDL-PCB congeners (PCB153, PCB52, PCB118, and PCB138) on cellular morphologies and synaptic transmission linked to the proper execution of a sensorimotor response in zebrafish, taking advantage of the well-established neural circuit in this model. Specifically, we imaged hair cells, neurons, and muscle tissue to evaluate their presence and morphology. We measured neurotransmitter levels in larvae and assessed the mechanosensory startle response in co-exposures to PCB153 and neurotransmitter modulators to evaluate the involvement of neurotransmitters in the behavioral response. The startle response was also assessed in dioxin-like (DL)-PCB126 exposed larvae. Results Startle responses were dramatically delayed in 6-day old larvae exposed to NDL-PCB. In contrast, exposure to the DL PCB126 did not delay startle response times. Morphological and biochemical data showed that exposure to NDL-PCBs during development induces swelling of afferent sensory neurons and disrupts dopaminergic and GABAergic signaling associated with motor movement. Discussion This study demonstrates that connections between neurotoxic mechanisms and processing of sensory stimuli occur at low concentrations of NDL-PCBs, similar to those present in human and animal samples. The effects on important and broadly conserved signaling mechanisms in vertebrates suggest that NDL-PCBs can contribute to neurodevelopmental abnormalities, relevant for both exposed human populations and wildlife.