To evaluate the efficiency of mesenchymal stem cells isolated from Wharton's jelly (WJ-MSCs) through either the intravenous or intraperitoneal transplantations into streptozotocin (STZ)-induced diabetic rats as a therapy for type 1 diabetes mellitus (T1DM). A rat model with STZ induction was established and the rats were divided into 3 groups: a tail vein injection group, an intraperitoneal injection group and a STZ control group. Following transplantation, blood glucose levels were monitored weekly then the pancreatic tissues were collected to examine the pancreatic islets by histopathology and morphometric studies. Intravenous transplantation of WJ-MSCs ameliorated hyperglycemia at day 7 after transplantation, with sustained decreased fasting blood glucose (FBG) levels until day 56. Further, these cells ameliorated at least partially the damage induced by STZ in the pancreas and produced a similar morphology to normal islets. On the contrary, intraperitoneal transplantation of WJ-MSCs failed to maintain normoglycemia or ameliorate the damaged pancreas in STZ-injected rats. These findings conclude that the intravenous administration method was effective in transplanting WJ-MSCs for the treatment of T1DM, whereas the intraperitoneal transplantation showed no therapeutic effect in our animal experiments.