This study assessed the health burden attributable to childhood underweight through 2050 focusing on disability-adjusted life years (DALYs), by considering the latest scenarios for climate change studies (representative concentration pathways and shared socioeconomic pathways (SSPs)) and conducting sensitivity analysis. A regression model for estimating DALYs attributable to childhood underweight (DAtU) was developed using the relationship between DAtU and childhood stunting. We combined a global computable general equilibrium model, a crop model, and two regression models to assess the future health burden. We found that (i) world total DAtU decreases from 2005 by 28 similar to 63% in 2050 depending on the socioeconomic scenarios. Per capita DAtU also decreases in all regions under either scenario in 2050, but the decreases vary significantly by regions and scenarios. (ii) The impact of climate change is relatively small in the framework of this study but, on the other hand, socioeconomic conditions have a great impact on the future health burden. (iii) Parameter uncertainty of the regression models is the second largest factor on uncertainty of the result following the changes in socioeconomic condition, and uncertainty derived from the difference in global circulation models is the smallest in the framework of this study.