Soybean oil-based intravenous fat emulsion (IVFE) administered to preterm neonates can induce oxidative stress and inflammatory response, which are associated with severe complications of prematurity. This study aimed to test the hypothesis that administration of medium-chain triglyceride (MCT)/ω-3 polyunsaturated fatty acid (PUFA)-enriched IVFE in preterm neonates is associated with a cytokine and fatty acid (FA) profile consistent with attenuated inflammatory response. In a double-blind randomized study, 60 preterm neonates (gestational age 26-32 weeks) were randomized to receive either MCT/ω-3 PUFA-enriched IVFE (intervention group) or soybean oil-based IVFE (control group). Serum biochemistry, tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-8, α-tocopherol, and FAs were assessed at baseline, on day of life 15, and day of life 30 or at the end of intervention. All cytokine levels changed significantly across the 3 time points, whereas the type of IVFE had a significant effect on final IL-6 and IL-8 levels, which were lower in the intervention group. The difference in final IL-6 and IL-8 levels remained significant after controlling for bronchopulmonary dysplasia and/or infection. α-Tocopherol and FA values changed significantly over time. MCT/ω-3 PUFA-enriched IVFE administration was associated with significantly higher α-tocopherol, eicosapentaenoic acid, docosahexaenoic acid, and ω-3 PUFAs and lower linolenic acid, total PUFA, and ω-6/ω-3 PUFA values compared with soybean oil-based IVFE. Both IVFEs were well tolerated. Compared with the soybean oil-based IVFE, the MCT/ω-3 PUFA-enriched IVFE is associated with a more favorable cytokine and FA profile consistent with attenuated inflammatory response in preterm neonates.