Acute kidney injury (AKI) has a negative impact on long-term renal function and prognosis. However, the association between acute renal dysfunction and long-term effects on bone disorders has not yet been characterized. Using a population-based cohort study, we aimed to evaluate associations between AKI and long-term effects on bone fractures. We identified relevant data of all hospitalized patients aged >18 years with histories of dialysis-requiring AKI, with subsequent recovery and discharge, from the claim records of the Taiwan National Health Insurance database between 2000 and 2008. We determined long-term de novo bone fracture and all-cause mortality after patients' index-hospitalization discharge using propensity score-adjusted Cox proportional hazard model. Varying-time models were used to adjust for long-term effects of end-stage renal disease (ESRD) on main outcomes. Among 448 AKI patients who had dialysis and survived 90 days after index-hospitalization discharge without reentering dialysis, 273 were male (60.9%) with a mean age of 61.4 ± 16.6 years. Controls included 1792 hospitalized patients without AKI, dialysis, or bone fracture history. In the AKI recovery group, bone fracture incidence was 320 per 10,000 person-years and hazard ratio (HR) of long-term bone fracture was 1.25 (p = 0.049) compared with the control group, independent of subsequent ESRD status (HR = 1.55; p = 0.01). Both AKI recovery status (HR = 2.31; p < 0.001) and time varying factor of bone fracture (HR = 1.43; p < 0.001) were independent predictors of mortality compared with controls. In conclusion, AKI requiring temporary dialysis independently increases long-term risk of bone fracture, regardless of subsequent progression to ESRD. Long-term bone fractures may negatively impact patient mortality.