Objective The relationship of antipsychotics and the risk of refracture in treated patients is unclear. The aim of this study is to evaluate the association between prolonged antipsychotic and the incidences of bone fractures and refractures in schizophrenia. Methods This is a retrospective nested case-control study using Taiwan National Health Insurance Research Database recorded from 2000 to 2005, with cases followed up to end of 2011. Total of 7,842 schizophrenic patients, 3,955 had developed bone fractures were compared with 3,887 control subjects matched in age, sex, and index date. Antipsychotic drug exposure was classified based on the drug type and medication duration. Conditional logistic regression analyses were performed. Odds ratio (OR) and confidence interval (CI) were calculated. Results We found (after adjustments) higher risks of developing fractures under continued use of typical (OR = 1.70; 95% CI, 1.51−1.91) or atypical antipsychotics (OR = 1.43; 95% CI, 1.28−1.60) were found. Additionally, continued use typical (OR = 1.84; 95% CI, 1.35−2.50) or atypical antipsychotics (OR = 1.44; 95% CI, 1.06−1.95) was positively associated with refracture risks. Moreover, refractures were associated with continuous use of chlorpromazine (one typical antipsychotics, OR = 2.45; 95% CI, 1.14−5.25), and risperidone (OR = 1.48; 95% CI, 1.01−2.16) or zotepine (OR = 2.15; 95% CI, 1.06−4.36) (two atypical antipsychotics). Conclusion Higher risks of bone fracture and refracture were found in schizophrenia under prolonged medication with typical or atypical antipsychotics. We therefore recommend that clinicians should pay more attention on bone density monitoring for patients using long-term antipsychotics.