Prepare the area by pulling furniture away from the wall and protecting the floor with a drop cloth.
Sand the paneling with a medium-fine sanding sponge, always working with the grain of the wood. Pay attention to scuffs and burn marks from the saw, since the stain highlights imperfections. Remove the sanding dust with a vacuum, soft brush or duster.
Apply pre-stain conditioner with a sponge or large brush, wait 5 to 10 minutes, and wipe away the excess with a lint-free rag. Without stain conditioner, the stain is likely to turn out blotchy on a soft, porous wood such as pine.
Apply stain immediately after wiping down the stain conditioner. Most conditioners require stain application right away; some allow you a window of time up to 2 hours. Once the conditioner has dried, the wood will not accept stain. Work in sections so you can apply the stain before the conditioner dries.
Apply oil-based stain with a natural-bristle brush or water-based stain with a synthetic brush. Choose a brush width about the same dimensions as the planks on the paneling, typically 3 or 4 inches wide.
Leave the stain on the paneling for 5 to 15 minutes. The longer you let it sit, the deeper the color.
Wipe the excess stain off with a lint-free rag. Allow the stained paneling to dry for at least 12 hours before hanging window treatments or putting anything back up on the walls.