Ethiopia recently scaled up the implementation of a school feeding program (SFP) as a targeted intervention for protecting disadvantaged school children from hunger and food insecurity. However, the contribution of the program to advancing the nutritional status of children has not been adequately explored. We assessed the effect of SFP on the anthropometric and haemoglobin status of school children in Sidama Region, Southern Ethiopia. Our prospective cohort study compared the height-for-age z-score (HAZ), BMI-for-age z-score (BAZ) and haemoglobin concentration of SFP beneficiary (n 240) and non-beneficiary (n 240) children, 10–14 years of age. The children were recruited from 8 SFP implementing and 8 control schools using a multistage sampling procedure and were followed for an academic year. The SFP intervention and control schools were matched one-to-one based on agro ecological features and geographical proximity. Exposure, outcome and pertinent extraneous variables were collected through baseline and end-line surveys. Multilevel difference-in-differences (DID) analysis was used to measure the net effect on the outcomes of interest. In the multivariable DID model adjusted for potential confounders including maternal and paternal literacy, household monthly income, wealth index and household food insecurity, the SFP did not show significant effects on the haemoglobin concentration (β = 0⋅251, 95 % confidence interval (CI): −0⋅238, 0⋅739), BAZ (β = 0⋅121, 95 % CI: −0⋅163, 0⋅405) and HAZ (β = −0⋅291, 95 % CI: −0⋅640, 0⋅588) of children.