A detailed understanding of the behaviour of confined fluids is critical to a range of industrial applications, for example to control friction in engineering components. In this study, a combination of tribological experiments and confined nonequilibrium molecular dynamics simulations has been used to investigate the effect of base fluid molecular structure on nonequilibrium phase behaviour and friction. An extensive parameter study, including several lubricant and traction fluid molecules subjected to pressures (0.5–2.0 GPa) and strain rates (104–1010 s−1) typical of the elastohydrodynamic lubrication regime, reveals clear relationships between the friction and flow behaviour. Lubricants, which are flexible, broadly linear molecules, give low friction coefficients that increase with strain rate and pressure in both the experiments and the simulations. Conversely, traction fluids, which are based on inflexible cycloaliphatic groups, give high friction coefficients that only weakly depend on strain rate and pressure. The observed differences in friction behaviour can be rationalised through the stronger shear localisation which is observed for the traction fluids in the simulations. Higher pressures lead to more pronounced shear localisation, whilst increased strain rates lead to a widening of the sheared region. The methods utilised in this study have clarified the physical mechanisms of important confined fluid behaviour and show significant potential in both improving the prediction of elastohydrodynamic friction and developing new molecules to control it.