A population balance model appropriate for the shear flow of thixotropic colloidal suspensions with yield stress is derived and tested against experimental data on a model system available in the literature. Modifications are made to account for dynamic arrest at the onset of the yield stress, in addition to enforcing a minimum particle size below which breakage is not feasible. The resulting constitutive model also incorporates a structural based relaxation time, unlike existing phenomenological models that use the inverse of the material shear rate as the relaxation time. The model provides a reasonable representation of experimental data for a model thixotropic suspension in the literature, capturing the important thixotropic timescales. When compared to prevalent structure kinetics models, the coarse-grained population balance equation is shown to be distinct, emphasizing the novelty of utilizing population balances as a basis for thixotropic suspension modeling. (c) 2016 American Institute of Chemical Engineers AIChE J, 63: 517-531, 2017