This study evaluated the effects of replacing fish oil (FO) with palm oil (PO) on enzyme activities and mRNA expression of lipid transport genes and signalling factors in juvenile Nile tilapia. Nile tilapia (9.34 ± 0.14 g) was fed five experimental diets with FO supplemented with PO at 0%, 25%, 50%, 75% and 100%. Liver was sampled from five fish per tank for analysis of fatty acids, enzyme activities and mRNA expression. Glucose 6‐phosphate dehydrogenase (G6PD) was highly expressed in groups fed higher levels of dietary PO, whilst liver X receptor (LXR) was highly expressed in groups fed lower levels of dietary PO. Groups fed 50% PO, 75% PO and 100% PO had significantly higher levels of G6PD mRNA expression whilst group fed 100% PO had significantly higher level of lipoprotein lipase (LPL) mRNA expression. Groups fed 75% PO and 100% PO recorded higher levels of PPAR‐α mRNA expression whilst higher level of malic enzyme mRNA expression was observed in group fed 75% PO. The mRNA expressions of the above stated genes and enzymes activities are predominantly influenced by dietary n‐3 PUFA and n‐6 PUFA levels. Dietary PO inclusion affected enzyme activities of LXR, PPAR‐α,PPAR‐β, LPL and FABP‐3. Activities of PPAR‐α, PPAR‐β and FABP‐3 were increased by PO inclusion whilst LXR and ELOVL 5 were reduced by PO inclusion. In conclusion, it could be inferred that substituting FO with PO could alter the metabolism pathway of genes such as LXR, G6PD, PPAR‐α, LPL and ME that are involved in the transport of fatty acids.