<b><i>Background:</i></b> Neonates undergoing surgery are at risk for uncontrolled inflammatory response and adverse clinical outcomes. Docosahexaenoic acid (DHA) ameliorates inflammation, improving clinical outcomes. However, its effect has not been evaluated in neonates undergoing surgery. We evaluated the effect of DHA on markers of inflammation and clinical outcomes in neonates undergoing surgery. <b><i>Methods:</i></b> A double-blind clinical trial evaluated the effect of enteral DHA (DHA group) versus sunflower oil (SO group) perioperatively administered in neonates scheduled for cardiovascular surgery. Inflammation was evaluated by percentage of cells⁺ for cytokines and CD69 in mononuclear cells at baseline, 24 h and 7 days post surgery. Clinical outcomes measured were sepsis, organ dysfunctions (ODs), length of stay in intensive care and bleeding. Repeated measures analysis of variance and logistic regression were applied. <b><i>Results:</i></b> Sixteen neonates received DHA and 18 received SO. Cells⁺ from neonates in the DHA group showed an early increase in receptor antagonist of interleukin (IL)-1⁺ (IL-1ra⁺) and IL-10⁺ and a late decrease in IL-6⁺. IL-1β⁺ and IL-10⁺ changes were different between groups. After adjusting for confounders, less cells from DHA group were IL-1β⁺, IL-6⁺, IL-1ra⁺ and IL-10⁺. DHA group presented less sepsis, ODs and shorter stay, but no difference in CD69⁺CD4⁺ cells or bleeding between groups. <b><i>Conclusions:</i></b> Administration of enteral DHA ameliorates markers of inflammation and improves clinical outcomes in surgical neonates.