This paper aims at providing further understanding on the fluid flow and heat transfer processes in unsteady rotating systems with mass transpiration. Such systems can be found in chemical separators, hydraulic systems, and printing devices. To this end, an unsteady viscous flow in the vicinity of an unaxisymmetric stagnation-point on a rotating cylinder is examined. The nonuniform transpiration and a transverse magnetic field are further considered. The angular speed of the cylinder and the thermal boundary conditions are expressed by time-dependent functions. A reduction of the Navier–Stokes and energy equations is obtained through using appropriate similarity transformations. The semisimilar solution of the Navier–Stokes equations and energy equation are developed numerically using an implicit finite difference scheme. Pertinent parameters including the Reynolds number and magnetic parameter and transpiration function are subsequently varied systematically. It is shown that the transpiration function can significantly affect the thermal and hydrodynamic behaviors of the system. In keeping with the findings in other areas of magnetohydrodynamics (MHD), the results show that the applied magnetic field has modest effects on the Nusselt number. However, it is demonstrated that the magnetic effects can significantly increase the imposed shear stress on the surface of the rotating cylinder.