The effect of vertical throughflow on the onset of penetrative convection simulated via internal heating in a two-layer system in which a layer of fluid overlies and saturates a layer of porous medium is studied. Flow in the porous medium is governed by Forchheimer-extended Darcy equation, and Beavers-Joseph slip condition is applied at the interface between the fluid and the porous layers. The boundaries are considered to be rigid, however permeable, and insulated to temperature perturbations. The eigenvalue problem is solved using a regular perturbation technique with wave number as a perturbation parameter. The ratio of fluid layer thickness to porous layer thickness, zeta, the direction of throughflow, and the presence of volumetric internal heat source in fluid and/or porous layer play a decisive role on the stability characteristics of the system. In addition, the influence of Prandtl number arising due to throughflow is also emphasized on the stability of the system. It is observed that both stabilizing and destabilizing factors can be enhanced because of the simultaneous presence of a volumetric heat source and vertical throughflow so that a more precise control (suppress or augment) of thermal convective instability in a layer of fluid or porous medium is possible.