This paper focusses on a theoretical analysis of the entropic generation and heat-transfer characteristics of electromagnetohydrodynamic (EMHD) flow in vertical hydrophobic microchannels. The flow viscosity, electrical conductivity, and thermal conductivity are assumed to be temperature variant. The fluid velocity and energy transfer equations associated with a system of coupled non-linear equations dealing with hydrophobic slip conditions are solved using a finite volume method associated with lubrication theory. The Debye–Hückel approximation is employed in an electrical double layer combined with the Poisson–Boltzmann equation to acquire an analytical solution for the electrical potential function. Slip velocities along with constant temperatures are provided to obtain numerical solutions for the case of a fully developed EMHD flow, in order to reveal the influence of fluid rheology. The results are presented for electromagnetic transport with variable viscosity over hydrophobic interfaces. Numerical and analytical validations are performed using the existing experimental results. In this study, we vizualize the significance of variable viscosity, electrical conductivity, and thermal conductivity on temperature distributions in the presence of a magnetic field. In this work, entropy generation is represented in terms of the Bejan number, which greatly impacts the normalized electroosmotic flow as well as the thermophysical parameters, leading to a minimization of the entropy-generation rate.