Engineering systems and materials do experience heating or cooling of some kind during operation. Modelling and theoretical analysis of heat transfer problems will enhance the functional success of the materials and enable new product development in engineering. The special issue on “Engineering Fluid Flows and Heat Transfer Analysis” of the journal “Diffusion Foundations” presents some novel theoretical analysis of various engineering heat transfer problems. Topics covered in this special issue include reactive fluid flow, magnetohydrodynamics, Newtonian and non-Newtonian fluid flow, natural convection, forced convection, mixed convection, porous media flow, and thermal radiation absorption effects.