Large-scale deworming interventions, using anthelminthic drugs, are recommended in areas where the prevalence of soil-transmitted helminth infection is high. Anthelminthic safety has been established primarily in school-age children. Our objective was to provide evidence on adverse events from anthelminthic use in early childhood. A randomized multi-arm, placebo-controlled trial of mebendazole, administered at different times and frequencies, was conducted in children 12 months of age living in Iquitos, Peru. Children were followed up to 24 months of age. The association between mebendazole administration and the occurrence of a serious or minor adverse event was determined using logistic regression. There was a total of 1,686 administrations of mebendazole and 1,676 administrations of placebo to 1,760 children. Eighteen serious adverse events (i.e., 11 deaths and seven hospitalizations) and 31 minor adverse events were reported. There was no association between mebendazole and the occurrence of a serious adverse event (odds ratio [OR] = 1.21; 95% confidence interval [CI] = 0.47, 3.09) or a minor adverse event (OR = 0.84; 95% CI = 0.41, 1.72). Results from our trial support evidence of safety in administering mebendazole during early childhood. These results support World Health Organization deworming policy and the scaling up of interventions to reach children as of 12 months of age in endemic areas.