Background There has been growing interest in understanding the role of agricultural trade policies in diet and nutrition. This cross-country study examines associations between government policies on agricultural trade prices and child nutrition outcomes, particularly undernutrition. Methods This study links panel data on government distortions to agricultural incentives to data from 212,258 children aged 6 to 35 months participating in Demographic and Health Surveys from 22 countries between 1991 and 2010. Country fixed-effects regression models were used to examine the association between within-country changes in nominal rates of assistance to tradable agriculture (government price distortions as a percentage of original prices) and child nutritional outcomes (height-for-age, weight-for-age, and weight-for-height Z-scores) while controlling for a range of time-varying country covariates. Results Five-year average nominal rates of assistance to tradable agriculture ranged from − 72.0 to 45.5% with a mean of − 5.0% and standard deviation of 18.9 percentage points. A 10-percentage point increase in five-year average rates of assistance to tradable agriculture was associated with improved height-for-age (0.02, 95% CI,0.00–0.05) and weight-for-age (0.05, 95% CI: 0.02–0.09) Z-scores. Improvements in nutritional status were greatest among children who had at least one parent earning wages in agriculture, and effects decreased as a country’s proportion of tradable agriculture increased, particularly for weight-for-age Z-scores. Conclusions Government assistance to tradable agriculture, such as through reduced taxation, was associated with small but significant improvements in child nutritional status, especially for children with a parent earning wages in agriculture when the share of tradable agriculture was not high. Electronic supplementary material The online version of this article (10.1186/s12992-019-0463-0) contains supplementary material, which is available to authorized users.