The present study examined the influence of a customized mouthguard on body alignment and balance performance in professional basketball players. Twenty-three professional male basketball players, aged 25.8 ± 8.6 years old, were voluntarily assigned to participate in three treatments, including no treatment (no mouthguard), acute treatment (wearing a mouthguard), and repeated treatments (8 weeks follow-up). Body alignment status, such as spinal and pelvic posture and balance performance, were measured at each time point using a 3D Formetric III (Germany) and a postural control device (Posturomed 202, Germany), respectively. A repeated MANOVA analysis with a Bonferroni post hoc test was applied, and the adjusted p-value was set at 0.02. No significant treatment effect was observed in body alignment (p = 0.302). However, univariate analysis showed a significant difference in pelvic torsion, where it was decreased after acute and repeated mouthguard treatments compared to no treatment (p < 0.001). Kyphotic angle also increased significantly following 8 weeks of treatment compared to no treatment (p < 0.001) and acute treatment (p < 0.002). There was a significant treatment effect on balance performance (p < 0.001). Both static and dynamic balance performance improved following 8 weeks of treatment (p < 0.001). Our study revealed that a customized mouthguard provides a benefit to balance performance. Notably, repeated treatment impacts on balance performance more than acute treatment. Although our findings did not show a significant effect on body alignment, some positive results, such as pelvic torsion and kyphotic angle, may provide substantial information for developing future longitudinal studies with large sample sizes.