Due to its high level of innervation, the lumbar facet capsular ligament (FCL) is suspected to play a role in low back pain (LBP). The nociceptors in the lumbar FCL may experience excessive deformation and generate pain signals. As such, understanding the mechanical behaviour of the FCL, as well as that of its underlying nerves, is critical if one hopes to understand its role in LBP. In this work, we constructed a multiscale structure-based finite-element (FE) model of a lumbar FCL on a spinal motion segment undergoing physiological motions of flexion, extension, ipsilateral and contralateral bending, and ipsilateral axial rotation. Our FE model was created for a generic FCL geometry by morphing a previously imaged FCL anatomy onto an existing generic motion segment model. The fibre organization of the FCL in our models was subject-specific based on previous analysis of six dissected specimens. The fibre structures from those specimens were mapped onto the FCL geometry on the motion segment. A motion segment model was used to determine vertebral kinematics under specified spinal loading conditions, providing boundary conditions for the FCL-only multiscale FE model. The solution of the FE model then provided detailed stress and strain fields within the tissue. Lastly, we used this computed strain field and our previous studies of deformation of nerves embedded in fibrous networks during simple deformations (e.g. uniaxial stretch, shear) to estimate the nerve deformation based on the local tissue strain and fibre alignment. Our results show that extension and ipsilateral bending result in largest strains of the lumbar FCL, while contralateral bending and flexion experience lowest strain values. Similar to strain trends, we calculated that the stretch of the microtubules of the nerves, as well as the forces exerted on the nerves' membrane are maximal for extension and ipsilateral bending, but the location within the FCL of peak microtubule stretch differed from that of peak membrane force.