Patient-specific nonlinear finite element analysis (FEA) is promising for evaluating the recovery of vertebral strength. Vertebral strength is closely related to inner vertebral stress distribution and is used to assess the fracture risk for individual osteoporotic patients during drug treatment. Moreover, stress distribution is affected by individual bone shape, bone density distribution and nonlinear behavior of the mechanical properties of bone. To investigate the effectiveness of FEA considering these factors for the evaluation of drug treatment effects, patient-specific nonlinear FEAs of the first lumbar vertebrae in patients undergoing a 3-year drug treatment were performed. Changes in fracture load and distribution of failure elements in the FE models at four time points (before therapy, and after 6 and 12 months and 3 years of therapy) were compared with those of average bone density. The FEAs demonstrated that failure elements decreased notably, and fracture load increased gradually by the 3-year time point, suggesting that the vertebrae were strengthened as a result of drug treatments. Furthermore, statistical tests indicated that mechanical evaluation using the nonlinear FEAs is more sensitive for evaluating drug effects on osteoporotic bone than assessments based on average bone density.