Scope Perinatal maternal moderately high‐fat diet (mHFD) is associated with obesity and fatty liver disease in offspring, and maternal fish oil (FO: n‐3 PUFA source) supplementation may attenuate these disorders. This study evaluates the effects of FO given to pregnant rats fed a mHFD on the offspring's liver at weaning. Methods and results Female Wistar rats receive an isoenergetic, control (CT: 10.9% from fat) or high‐fat (HF: 28.7% from fat) diet before mating, and throughout pregnancy and lactation. FO supplementation (HFFO: 2.9% of FO in the HF diet) is given to one subgroup of HF dams during pregnancy. At weaning, male and female mHFD offspring display higher body mass, adiposity, and hepatic cellular damage, steatosis, and inflammation, accompanied by increased damaged mitochondria. FO does not protect pups from systemic metabolic alterations and partially mitigates hepatic histological damage induced by mHFD only in females. However, FO reduces mRNA expression of lipogenic genes, and mitochondrial damage, and modified mitochondrial morphology suggestive of early adaptations via mitochondrial dynamics. Conclusions Gestational FO supplementation has limited beneficial effects on the damage caused by perinatal mHFD consumption in offspring's liver at weaning. However, FO imprinting effect on lipid metabolism and mitochondria may have beneficial long‐term outcomes. Maternal fish oil gestational supplementation to rats fed a high‐fat diet from pre‐gestation throughout lactation didn't prevent offspring's obesogenic profile at weaning. Fish oil partially mitigated liver histopathological damage in females, but not in males. However, it reduces lipogenic genes expression and mitochondrial damage in both sexes, and induces adaptive changes in mitochondria morphology and dynamics markers with sex differences.