The outstanding lubrication of articular cartilage in the major synovial joints such as hips and knees, essential for the joint well-being, has been attributed to boundary layers of lipids at the outer cartilage surfaces, which have very low friction mediated by the hydration lubrication mechanism at their highly hydrated exposed headgroups. However, the role of spontaneously present lipid splays—lipids with an acyl tail in each of the opposing bilayers—in modulating the frictional force between lipid bilayers has not, to date, been considered. In this study, we perform all-atom molecular dynamics simulations to quantitatively assess the significance of splayed molecules within the framework of lubricating lipid bilayers. We demonstrate that, although transient, splayed molecules significantly increase the inter-membrane friction until their retraction back into the lamellar phase, with this effect more steadily occurring at lower sliding velocities that are comparable to the physiological velocities of sliding articular cartilage.