In low-income countries early measles vaccine (MV) is associated with reduced child mortality which cannot be explained by prevention of measles. A large thymus gland in infancy is also associated with reduced mortality. We hypothesized that early MV is associated with increased thymic size. Within a randomized trial providing MV at age 4.5 and 9 months or MV only at age 9 months, thymic size was assessed by ultrasound at age 4.5 months, before randomization to early MV or no early MV, and 4 weeks later. Among 656 children, there was no effect of early MV on thymic size, the geometric mean size ratio being 0.99 (95% CI: 0.96-1.02). In a post hoc analysis early MV was associated with a negative effect in healthy children but a positive effect in ill children. In conclusion, early MV at age 4.5 months had no overall effect on thymus size 4 weeks later. Trial registration: http://clinicaltrials.gov, NCT01486355.