An attempt is made in this work to combine the Lennard–Jones chain model (LJC) of self-diffusion coefficient with the statistical associating fluid theory (SAFT). The real non-spherical associating molecules are modeled as chains of tangent Lennard–Jones segments with association sites. An equation for the self-diffusion coefficient in a polyatomic associating fluid is presented as a product of a non-hydrogen-bond contribution and a hydrogen-bond contribution. The SAFT equation provides the density and temperature dependence of an average number of hydrogen bonds in a molecule, and the LJC equation is used to calculate the self-diffusion coefficient for a non-associating fluid. The segment–segment interaction energy ε is obtained from the critical temperature for alcohols and hydrogen fluoride, and, the segment diameter σ, the chain length N (the number of segments), association energy εHB and volume κHB are determined from the experimental diffusion data. The equation reproduces the experimental self-diffusion coefficient with total average absolute deviation of 6.69% for water, 6% alcohols and hydrogen fluoride over wide ranges of temperature and pressure, including the super-critical water.