The retinal pigment epithelium‐specific 65 kDa (RPE65) isomerase plays a pivotal role in photoreceptor survival and function. RPE65‐catalyzed synthesis of 11‐cis‐retinol from all‐trans‐retinyl esters in the visual cycle is negatively regulated, through a heretofore unknown mechanism, by the fatty acid transport protein FATP4, mutations in which are associated with ichthyosis prematurity syndrome (IPS). Here, we analyzed the interaction between deletion mutants of FATP4 and RPE65 and the impacts of IPS‐associated FATP4 mutations on RPE65 expression, 11‐cis‐retinol synthesis, and all‐trans‐retinyl ester synthesis. Our results suggest that the interaction between FATP4 and RPE65 contributes to the inhibition of RPE65 function and that IPS‐associated nonsense and missense mutations in FATP4 have different effects on the visual cycle.