Alignment of anisotropic supermolecular building blocks is crucial to control the properties of many novel materials. In this study, the alignment process of cellulose nanofibrils (CNFs) in a flow-focusing channel has been investigated using small-angle X-ray scattering (SAXS) and modeled using the Smoluchowski equation, which requires a known flow field as input. This flow field was investigated experimentally using microparticle-tracking velocimetry and by numerically applying the two-fluid level set method. A semidilute dispersion of CNFs was modeled as a continuous phase, with a higher viscosity as compared to that of water. Furthermore, implementation of the Smoluchowski equation also needed the rotational Brownian diffusion coefficient, which was experimentally determined in a shear viscosity measurement. The order of the nanofibrils was found to increase during extension in the flow-focusing channel, after which rotational diffusion acted on the orientation distribution, driving the orientation of the fibrils toward isotropy. The main features of the alignment and dealignment processes were well predicted by the numerical model, but the model overpredicted the alignment at higher rates of extension. The apparent rotational diffusion coefficient was seen to increase steeply as the degree of alignment increased. Thus, the combination of SAXS measurements and modeling provides the necessary framework for quantified studies of hydrodynamic alignment, followed by relaxation toward isotropy.