Purchase flexible roof flashing compatible with the size of your stove pipe and the pitch and material of your roof. Some designs are composed of silicone that can permit temperatures as high as 480 F. Other products can only permit temperatures to 240 F. Use the best product for your situation. Models with rectangular bases can fit whether the hole is square or circular. Circular bases are also available.
Place the rubber cone of the flashing over the stove pipe and note where the cone should be cut so the pipe can fit through. Cut the circle out with tin snips.
Slide the cone down the pipe, using water to lubricate the pipe if necessary.
Apply silicone sealant around all edges of the underside of the flange, which is the base of the flashing.
Press the flange down so it conforms with the texture of your roof. Flatten and smooth out any creases that appear. The flange on metal roof flashing is composed of aluminum, silicone or other flexible materials.
Secure flashing with self-tapping screws, according to manufacturer instructions.