The boundary effect on the electrophoretic behavior of a particle in a non-Newtonian fluid is studied by considering the electrophoresis of a finite rod along the axis of a cylindrical microchannel filled with shear-thinning Carreau fluids, which include both Newtonian and power-law fluids as special cases. Under the conditions of low surface potential and weak applied electric field, the influences of the radius of the microchannel, the aspect ratio of the rod, the thickness of double layer, and the nature of the Carreau fluid on the mobility of the rod are investigated. We show that due to the shear-thinning effect, the mobility of the rod in the present case can be significantly larger than that in the corresponding Newtonian case; the former is more sensitive to the variation in the thickness of double layer than the latter, and the difference between the two increases with decreasing thickness of double layer. The shear-thinning effect is important under the following conditions: the double layer is thin, the boundary effect is important, and/or the aspect ratio is large. We show that increasing the aspect ratio can either raise or lessen its mobility, which is not found previously, and can play an important role in electrophoresis measurement.