Runoff is an important water flux that is difficult to simulate and predict due to lacking observation. Meteorological forcing data are a key factor in causing the uncertainty of predicted runoff. In this study, climate projections from ten general circulation models of the Coupled Model Intercomparison Project 5 (CMIP5) with high resolution under the Representative Concentration Pathway (RCP) 4.5 scenario are employed to estimate the future uncertainty range of predicted runoff in the North–South Transect of Eastern China (NSTEC) from 2011 to 2100. It is found that the range of future annual runoff is from 268.9 mm (Meteorological Research Institute coupled GCM, MRI-CGCM3) to 544.2 mm (Model for Interdisciplinary Research on Climate, MIROC5). The precipitation and the annual actual evapotranspiration are two key factors that affect the variation of runoff. The low annual runoff for the MRI-CGCM3 model may be caused by low precipitation and high annual actual evapotranspiration (466.9 mm). However, the high annual runoff for the MIROC5 may be caused by the high precipitation, although there is high annual actual evapotranspiration (544.2 mm). The above results imply that the forcing data and the model physics are important factors in the numerical simulation and prediction about runoff.