Epilepsy, a common disorder of the brain, exhibits a high morbidity rate in children. Childhood epilepsy (CE) is frequently comorbid with neurologic and developmental disorders, sharing underlying genetic factors. This study aimed to investigate the impact of
ADORA2A
,
BDNF
, and
NTRK2
gene polymorphisms on the risk of childhood epilepsy and their associations with predisposition to epileptic comorbidities. A total of 444 children were enrolled in this study, and three single nucleotide polymorphisms, including
ADORA2A
rs2298383,
BDNF
rs6265, and
NTRK2
rs1778929, were genotyped. The frequency distribution of genotypes was compared not only between CE patients and healthy children but also between CE patients with and without comorbidities. The results indicated that the carriers of
ADORA2A
rs2298383 TT genotype tended to have a lower risk of epilepsy (OR = 0.48, 95% CI = 0.30–0.76), while the CT genotype was related to a higher risk (OR = 1.56, 95% CI = 1.06–2.27). The
ADORA2A
rs2298383 CC genotype predisposed CE patients to comorbid neurologic disorders (OR = 2.76, 95% CI = 1.31–5.80). Genetic variations in
BDNF
rs6265 and
NTRK2
rs1778929 had no significant association with CE and its comorbidities. Fourteen ADORA2A target genes related to epilepsy were identified by the protein–protein interaction analysis, which were mainly involved in the biological processes of “negative regulation of neuron death” and “purine nucleoside biosynthetic process” through the gene functional enrichment analysis. Our study revealed that the genetic polymorphism of
ADORA2A
rs2298383 was associated with CE risk and predisposition to neurologic comorbidity in children with epilepsy, and the involved mechanism might be related to the regulation of neuron death and purine nucleoside biosynthesis.