Objective To provide appropriate evaluation methods and accurate data support for the study of pediatric nervous system drugs, the functional observation battery (FOB) was used to evaluate the effects of different nervous system drugs on juvenile Beagle dogs. Methods Juvenile Beagle dogs were randomly assigned to negative control group, nikethamide group (25 mg/kg), caffeine group (30 mg/kg), and phenobarbital group (12 mg/kg). All groups received a single administration: the negative control group was administered 0.9% sodium chloride injection, while the other groups received their respective drugs. FOB assessments were conducted at baseline (pre-dose) and at 1 h, 2 h, and 3 h post-dose. Results Following drug intervention, compared with the negative control group, the nikethamide group exhibited increased respiratory rate and enhanced responses to facial sensory examination score (P < 0.05), with vomiting observed in 1/6 animals; the caffeine group showed increased respiratory rate, elevated responses to visual/auditory stimuli, and accelerated proprioceptive positioning response (P < 0.05), along with abnormal hypoglossal reflex in 1/6 animals and stereotyped behavior in 3/6 animals (P < 0.05); the phenobarbital group demonstrated decreased neck muscle tone, limb tone, and slowed proprioceptive positioning response (P < 0.05), with reduced muscle stretch reflex, triceps reflex, and patellar reflex (P < 0.05). Conclusion Under the experimental conditions of this study, we consider the FOB method to be a suitable approach for evaluating the toxicity of pediatric nervous system drugs in juvenile Beagle dogs. It effectively identified specific toxic manifestations induced by commonly used clinical nervous system drugs such as nikethamide, caffeine, and phenobarbital.