Lithium is regarded as the first-line treatment for bipolar disorder (BD), a severe and disabling mental health disorder that affects about 1% of the population worldwide. Nevertheless, lithium is not consistently effective, with only 30% of patients showing a favorable response to treatment. To provide personalized treatment options for bipolar patients, it is essential to identify prediction biomarkers such as polygenic scores. In this study, we developed a polygenic score for lithium treatment response (Li ⁺ _PGS ) in patients with BD. To gain further insights into lithium’s possible molecular mechanism of action, we performed a genome-wide gene-based analysis. Using polygenic score modeling, via methods incorporating Bayesian regression and continuous shrinkage priors, Li ⁺ _PGS was developed in the International Consortium of Lithium Genetics cohort (ConLi ⁺ Gen: N = 2367) and replicated in the combined PsyCourse ( N = 89) and BipoLife ( N = 102) studies. The associations of Li ⁺ _PGS and lithium treatment response — defined in a continuous ALDA scale and a categorical outcome (good response vs. poor response) were tested using regression models, each adjusted for the covariates: age, sex, and the first four genetic principal components. Statistical significance was determined at P < 0.05. Li ⁺ _PGS was positively associated with lithium treatment response in the ConLi ⁺ Gen cohort, in both the categorical ( P = 9.8 × 10 ^{− 12} , R ² = 1.9%) and continuous ( P = 6.4 × 10 ^{− 9} , R ² = 2.6%) outcomes. Compared to bipolar patients in the 1 ^st decile of the risk distribution, individuals in the 10 ^th decile had 3.47-fold (95%CI: 2.22–5.47) higher odds of responding favorably to lithium. The results were replicated in the independent cohorts for the categorical treatment outcome ( P = 3.9 × 10 ^{− 4} , R ² = 0.9%), but not for the continuous outcome ( P = 0.13). Gene-based analyses revealed 36 candidate genes that are enriched in biological pathways controlled by glutamate and acetylcholine. Li ⁺ _PGS may be useful in the development of pharmacogenomic testing strategies by enabling a classification of bipolar patients according to their response to treatment.