Ultra-long-chain fatty acids (ULCFAs) are biosynthesized in certain types of tissues, but their biological roles remain unknown. Here, we report how the conformation of ULCFAs depends on the length and unsaturated-bond ratio of the ultra-long chains and the composition of the host bilayer membrane using molecular dynamics simulations. The ultra-long chain of ULCFAs flips between the two leaflets and fluctuates among three conformations: elongated, L-shaped, and turned. Furthermore, we found that the saturated ultra-long chain exhibited an elongated conformation more frequently than the unsaturated chain. In addition, the truncation of the ultra-long chain at C26 had little effect on the remaining ULCFAs. ULCFAs respond to lipid-density differences in the two leaflets, and the ratio of the elongated and turned conformations changed to reduce this difference. However, in cholesterol-containing membranes, ULCFAs exhibit no density difference after the flip-flop of cholesterol removes the difference.